From 9eecb39534fff6e33811345aad2ee8568520f8de Mon Sep 17 00:00:00 2001 From: "renovate[bot]" Date: Wed, 26 Jul 2023 11:01:30 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20tongzhug?= =?UTF-8?q?roup/tongzhugroup.github.io@70c4cea8c5f743208f46be20290a6dbc153?= =?UTF-8?q?c9694=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 2018/06/18/welcome-to-our-new-website/index.html | 2 +- .../index.html | 2 +- .../index.html | 2 +- .../index.html" | 2 +- 2019/01/14/our-work-on-metal-mfcc-got-accepeted/index.html | 2 +- 2019/02/27/congratulations-to-yu-and-jinzhe/index.html | 2 +- .../index.html | 2 +- .../index.html | 2 +- .../index.html | 2 +- 2020/05/21/elementor-677/index.html | 2 +- archives/2018/06/index.html | 2 +- archives/2018/07/index.html | 2 +- archives/2018/12/index.html | 2 +- archives/2018/index.html | 2 +- archives/2019/01/index.html | 2 +- archives/2019/02/index.html | 2 +- archives/2019/05/index.html | 2 +- archives/2019/06/index.html | 2 +- archives/2019/07/index.html | 2 +- archives/2019/index.html | 2 +- archives/2020/05/index.html | 2 +- archives/2020/index.html | 2 +- archives/index.html | 2 +- categories/News/index.html | 2 +- categories/uncategorized/index.html | 2 +- .../index.html" | 2 +- elementor-612/index.html | 2 +- group-seminar/index.html | 2 +- index.html | 2 +- memory/index.html | 2 +- people/index.html | 2 +- publications/index.html | 2 +- reacnetgenerator/index.html | 2 +- research/index.html | 2 +- sitemap.xml | 6 +++--- softwares/index.html | 2 +- teaching/index.html | 2 +- tips/index.html | 2 +- .../index.html" | 2 +- 39 files changed, 41 insertions(+), 41 deletions(-) diff --git a/2018/06/18/welcome-to-our-new-website/index.html b/2018/06/18/welcome-to-our-new-website/index.html index 5482bc7aa..aec5837a8 100644 --- a/2018/06/18/welcome-to-our-new-website/index.html +++ b/2018/06/18/welcome-to-our-new-website/index.html @@ -1 +1 @@ -Welcome to our new website! | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

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\ No newline at end of file +Welcome to our new website! | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

0%
\ No newline at end of file diff --git a/2018/07/07/our-recent-work-on-the-conformational-dynamics-of-prion-available-online-now/index.html b/2018/07/07/our-recent-work-on-the-conformational-dynamics-of-prion-available-online-now/index.html index 2a2dc9a4c..53e66af7b 100644 --- a/2018/07/07/our-recent-work-on-the-conformational-dynamics-of-prion-available-online-now/index.html +++ b/2018/07/07/our-recent-work-on-the-conformational-dynamics-of-prion-available-online-now/index.html @@ -1 +1 @@ -Our recent work on the conformational dynamics of Prion available online now | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

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\ No newline at end of file +Our recent work on the conformational dynamics of Prion available online now | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

0%
\ No newline at end of file diff --git a/2018/07/07/tong-attended-the-wccb-2018-and-honored-the-best-poster-award/index.html b/2018/07/07/tong-attended-the-wccb-2018-and-honored-the-best-poster-award/index.html index 8bc84f9e9..b8b545012 100644 --- a/2018/07/07/tong-attended-the-wccb-2018-and-honored-the-best-poster-award/index.html +++ b/2018/07/07/tong-attended-the-wccb-2018-and-honored-the-best-poster-award/index.html @@ -1 +1 @@ -Tong attended the WCCB 2018 and honored the Best Poster Award | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

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\ No newline at end of file +Tong attended the WCCB 2018 and honored the Best Poster Award | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

0%
\ No newline at end of file diff --git "a/2018/12/10/tong-attended-the-2018\345\244\215\346\235\202\344\275\223\347\263\273\350\256\241\347\256\227\347\273\237\350\256\241\345\212\233\345\255\246\347\240\224\350\256\250\344\274\232-and-gave-a-talk-about-the-force-field-development-for-me/index.html" "b/2018/12/10/tong-attended-the-2018\345\244\215\346\235\202\344\275\223\347\263\273\350\256\241\347\256\227\347\273\237\350\256\241\345\212\233\345\255\246\347\240\224\350\256\250\344\274\232-and-gave-a-talk-about-the-force-field-development-for-me/index.html" index 7e653c0af..4f4755856 100644 --- "a/2018/12/10/tong-attended-the-2018\345\244\215\346\235\202\344\275\223\347\263\273\350\256\241\347\256\227\347\273\237\350\256\241\345\212\233\345\255\246\347\240\224\350\256\250\344\274\232-and-gave-a-talk-about-the-force-field-development-for-me/index.html" +++ "b/2018/12/10/tong-attended-the-2018\345\244\215\346\235\202\344\275\223\347\263\273\350\256\241\347\256\227\347\273\237\350\256\241\345\212\233\345\255\246\347\240\224\350\256\250\344\274\232-and-gave-a-talk-about-the-force-field-development-for-me/index.html" @@ -1 +1 @@ -Tong attended the "2018复杂体系计算统计力学研讨会" and gave a talk about the force field development for metallopoteins. | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

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\ No newline at end of file +Tong attended the "2018复杂体系计算统计力学研讨会" and gave a talk about the force field development for metallopoteins. | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

0%
\ No newline at end of file diff --git a/2019/01/14/our-work-on-metal-mfcc-got-accepeted/index.html b/2019/01/14/our-work-on-metal-mfcc-got-accepeted/index.html index c11f48b62..9472a4fb4 100644 --- a/2019/01/14/our-work-on-metal-mfcc-got-accepeted/index.html +++ b/2019/01/14/our-work-on-metal-mfcc-got-accepeted/index.html @@ -1 +1 @@ -Our work on Metal-MFCC got accepeted | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

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\ No newline at end of file +Our work on Metal-MFCC got accepeted | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

0%
\ No newline at end of file diff --git a/2019/02/27/congratulations-to-yu-and-jinzhe/index.html b/2019/02/27/congratulations-to-yu-and-jinzhe/index.html index c5859fd49..e24ad684b 100644 --- a/2019/02/27/congratulations-to-yu-and-jinzhe/index.html +++ b/2019/02/27/congratulations-to-yu-and-jinzhe/index.html @@ -1 +1 @@ -Congratulations to Yu and Jinzhe | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

0%
\ No newline at end of file +Congratulations to Yu and Jinzhe | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

0%
\ No newline at end of file diff --git a/2019/05/17/congratulations-to-pei-yu-yanping-and-jinzhe-on-graduation/index.html b/2019/05/17/congratulations-to-pei-yu-yanping-and-jinzhe-on-graduation/index.html index ddd7a29ed..581b545ea 100644 --- a/2019/05/17/congratulations-to-pei-yu-yanping-and-jinzhe-on-graduation/index.html +++ b/2019/05/17/congratulations-to-pei-yu-yanping-and-jinzhe-on-graduation/index.html @@ -1 +1 @@ -Congratulations to Pei, Yu, Yanping, and Jinzhe on graduation! | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

0%
\ No newline at end of file +Congratulations to Pei, Yu, Yanping, and Jinzhe on graduation! | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

0%
\ No newline at end of file diff --git a/2019/06/08/our-recent-work-effect-of-mutations-on-binding-of-ligands-to-guanine-riboswitch-probed-by-free-energy-perturbation-and-molecular-dynamics-simulations-available-online-now/index.html b/2019/06/08/our-recent-work-effect-of-mutations-on-binding-of-ligands-to-guanine-riboswitch-probed-by-free-energy-perturbation-and-molecular-dynamics-simulations-available-online-now/index.html index b85fc5e70..6ba52c9a5 100644 --- a/2019/06/08/our-recent-work-effect-of-mutations-on-binding-of-ligands-to-guanine-riboswitch-probed-by-free-energy-perturbation-and-molecular-dynamics-simulations-available-online-now/index.html +++ b/2019/06/08/our-recent-work-effect-of-mutations-on-binding-of-ligands-to-guanine-riboswitch-probed-by-free-energy-perturbation-and-molecular-dynamics-simulations-available-online-now/index.html @@ -1 +1 @@ -Our recent work "Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations" available online now. | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

0%
\ No newline at end of file +Our recent work "Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations" available online now. | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

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\ No newline at end of file diff --git a/2019/07/22/our-recent-work-molecular-dynamics-simulation-of-zinc-ion-in-water-with-an-ab-initio-based-neural-network-potential-available-online-now/index.html b/2019/07/22/our-recent-work-molecular-dynamics-simulation-of-zinc-ion-in-water-with-an-ab-initio-based-neural-network-potential-available-online-now/index.html index 5f962af15..adc086cee 100644 --- a/2019/07/22/our-recent-work-molecular-dynamics-simulation-of-zinc-ion-in-water-with-an-ab-initio-based-neural-network-potential-available-online-now/index.html +++ b/2019/07/22/our-recent-work-molecular-dynamics-simulation-of-zinc-ion-in-water-with-an-ab-initio-based-neural-network-potential-available-online-now/index.html @@ -1 +1 @@ -Our recent work "Molecular Dynamics Simulation of Zinc Ion in Water with an ab Initio Based Neural Network Potential" available online now. | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

0%
\ No newline at end of file +Our recent work "Molecular Dynamics Simulation of Zinc Ion in Water with an ab Initio Based Neural Network Potential" available online now. | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

0%
\ No newline at end of file diff --git a/2020/05/21/elementor-677/index.html b/2020/05/21/elementor-677/index.html index 07127c52c..57d8ee7c6 100644 --- a/2020/05/21/elementor-677/index.html +++ b/2020/05/21/elementor-677/index.html @@ -1 +1 @@ -热风 | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

热风

Posted on In
愿中国青年都摆脱冷气，只是向上走 不必听自暴自弃者流的话 能做事的做事，能发声的发声 有一分热，发一分光，就令萤火一般，也可以在黑暗里发一点光，不必等候炬火 此后如竟没有炬火：我便是唯一的光 倘若有了炬火，出了太阳，我们自然心悦诚服的消失 不但毫无不平，而且还要随喜赞美这炬火或太阳 因为他照了人类，连我都在内。
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\ No newline at end of file +热风 | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

热风

Posted on In
愿中国青年都摆脱冷气，只是向上走 不必听自暴自弃者流的话 能做事的做事，能发声的发声 有一分热，发一分光，就令萤火一般，也可以在黑暗里发一点光，不必等候炬火 此后如竟没有炬火：我便是唯一的光 倘若有了炬火，出了太阳，我们自然心悦诚服的消失 不但毫无不平，而且还要随喜赞美这炬火或太阳 因为他照了人类，连我都在内。
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\ No newline at end of file diff --git a/archives/2018/06/index.html b/archives/2018/06/index.html index 56f9a7eb0..f17c93b4a 100644 --- a/archives/2018/06/index.html +++ b/archives/2018/06/index.html @@ -1 +1 @@ -Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2018
0%
\ No newline at end of file +Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2018
0%
\ No newline at end of file diff --git a/archives/2018/07/index.html b/archives/2018/07/index.html index 070bd646c..ad241697f 100644 --- a/archives/2018/07/index.html +++ b/archives/2018/07/index.html @@ -1 +1 @@ -Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2018
0%
\ No newline at end of file +Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2018
0%
\ No newline at end of file diff --git a/archives/2018/12/index.html b/archives/2018/12/index.html index 3543dc51d..e9e228068 100644 --- a/archives/2018/12/index.html +++ b/archives/2018/12/index.html @@ -1 +1 @@ -Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2018
0%
\ No newline at end of file +Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2018
0%
\ No newline at end of file diff --git a/archives/2018/index.html b/archives/2018/index.html index 8732f989f..9bec300b2 100644 --- a/archives/2018/index.html +++ b/archives/2018/index.html @@ -1 +1 @@ -Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2018
0%
\ No newline at end of file +Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2018
0%
\ No newline at end of file diff --git a/archives/2019/01/index.html b/archives/2019/01/index.html index 373329b02..cb781cc16 100644 --- a/archives/2019/01/index.html +++ b/archives/2019/01/index.html @@ -1 +1 @@ -Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2019
0%
\ No newline at end of file +Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2019
0%
\ No newline at end of file diff --git a/archives/2019/02/index.html b/archives/2019/02/index.html index 6de5084f2..811ecb1df 100644 --- a/archives/2019/02/index.html +++ b/archives/2019/02/index.html @@ -1 +1 @@ -Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2019
0%
\ No newline at end of file +Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2019
0%
\ No newline at end of file diff --git a/archives/2019/05/index.html b/archives/2019/05/index.html index f7cd6fba7..b426a84d6 100644 --- a/archives/2019/05/index.html +++ b/archives/2019/05/index.html @@ -1 +1 @@ -Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2019
0%
\ No newline at end of file +Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2019
0%
\ No newline at end of file diff --git a/archives/2019/06/index.html b/archives/2019/06/index.html index 1f544f12b..9b8cc40dd 100644 --- a/archives/2019/06/index.html +++ b/archives/2019/06/index.html @@ -1 +1 @@ -Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2019
0%
\ No newline at end of file +Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2019
0%
\ No newline at end of file diff --git a/archives/2019/07/index.html b/archives/2019/07/index.html index 7cb84fd77..8816cb67d 100644 --- a/archives/2019/07/index.html +++ b/archives/2019/07/index.html @@ -1 +1 @@ -Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2019
0%
\ No newline at end of file +Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2019
0%
\ No newline at end of file diff --git a/archives/2019/index.html b/archives/2019/index.html index b18563b29..8d149b652 100644 --- a/archives/2019/index.html +++ b/archives/2019/index.html @@ -1 +1 @@ -Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2019
0%
\ No newline at end of file +Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2019
0%
\ No newline at end of file diff --git a/archives/2020/05/index.html b/archives/2020/05/index.html index 95cea358d..041324f9a 100644 --- a/archives/2020/05/index.html +++ b/archives/2020/05/index.html @@ -1 +1 @@ -Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2020
0%
\ No newline at end of file +Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2020
0%
\ No newline at end of file diff --git a/archives/2020/index.html b/archives/2020/index.html index d2545e2bb..3e480a0af 100644 --- a/archives/2020/index.html +++ b/archives/2020/index.html @@ -1 +1 @@ -Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2020
0%
\ No newline at end of file +Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2020
0%
\ No newline at end of file diff --git a/archives/index.html b/archives/index.html index 9a1146d43..6aa39e06e 100644 --- a/archives/index.html +++ b/archives/index.html @@ -1 +1 @@ -Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2020
2019
2018
0%
\ No newline at end of file +Archive | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Um..! 10 posts in total. Keep on posting.
2020
2019
2018
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\ No newline at end of file diff --git a/categories/News/index.html b/categories/News/index.html index da2eb348e..da12792f4 100644 --- a/categories/News/index.html +++ b/categories/News/index.html @@ -1 +1 @@ -Category: News | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

News Category

2019
2018
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\ No newline at end of file +Category: News | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

News Category

2019
2018
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\ No newline at end of file diff --git a/categories/uncategorized/index.html b/categories/uncategorized/index.html index 3e4f7c6a8..967adbb63 100644 --- a/categories/uncategorized/index.html +++ b/categories/uncategorized/index.html @@ -1 +1 @@ -Category: uncategorized | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

uncategorized Category

2020
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\ No newline at end of file +Category: uncategorized | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

uncategorized Category

2020
0%
\ No newline at end of file diff --git "a/centos7-\346\272\220\344\273\243\347\240\201\345\256\211\350\243\205pymol-\357\274\210install-pymol-from-source-code-on-centos7\357\274\211/index.html" "b/centos7-\346\272\220\344\273\243\347\240\201\345\256\211\350\243\205pymol-\357\274\210install-pymol-from-source-code-on-centos7\357\274\211/index.html" index bcaae0ea4..efcc82255 100644 --- "a/centos7-\346\272\220\344\273\243\347\240\201\345\256\211\350\243\205pymol-\357\274\210install-pymol-from-source-code-on-centos7\357\274\211/index.html" +++ "b/centos7-\346\272\220\344\273\243\347\240\201\345\256\211\350\243\205pymol-\357\274\210install-pymol-from-source-code-on-centos7\357\274\211/index.html" @@ -1 +1 @@ -CentOS7 源代码安装pymol （install pymol from source code on CentOS7） | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

CentOS7 源代码安装pymol （install pymol from source code on CentOS7）

1. yum install gcc gcc-c++ kernel-devel python-devel tkinter python-pmw glew-devel \
freeglut-devel libpng-devel freetype-devel libxml2-devel glm-devel python3-devel netcdf-devel
2. install Anaconda3
3. git clone https://github.com/schrodinger/pymol-open-source.git
4. git clone https://github.com/rcsb/mmtf-cpp.git mv mmtf-cpp/include/mmtf* pymol-open-source/include/
5. cd pymol-open-source
6. export prefix=$HOME/pymol_src
7. python3 setup.py build install –home=$prefix

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\ No newline at end of file +CentOS7 源代码安装pymol （install pymol from source code on CentOS7） | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

CentOS7 源代码安装pymol （install pymol from source code on CentOS7）

1. yum install gcc gcc-c++ kernel-devel python-devel tkinter python-pmw glew-devel \
freeglut-devel libpng-devel freetype-devel libxml2-devel glm-devel python3-devel netcdf-devel
2. install Anaconda3
3. git clone https://github.com/schrodinger/pymol-open-source.git
4. git clone https://github.com/rcsb/mmtf-cpp.git mv mmtf-cpp/include/mmtf* pymol-open-source/include/
5. cd pymol-open-source
6. export prefix=$HOME/pymol_src
7. python3 setup.py build install –home=$prefix

0%
\ No newline at end of file diff --git a/elementor-612/index.html b/elementor-612/index.html index 833e515ac..b5d335e0f 100644 --- a/elementor-612/index.html +++ b/elementor-612/index.html @@ -1 +1 @@ -CP2K6.1 Install | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

CP2K6.1 Install

CP2K 6.1 编译安装 (Intel 编译器)

CP2K 6.1.0-release 多进程多线程(MPI+OPENMP)

制作者：曹立群

更新时间：2019.10.09

测试版本：CP2K 6.1.0-release

本文基于前辈安装老版本的说明撰写：

https://blog.csdn.net/zh314js/article/details/76258705

1.下载并安装intel编译器(最新版本2019)

安装后在~/.bashrc添加:

source /opt/intel/compilers_and_libraries_2017.4.196/linux/bin/ifortvars.sh intel64

source /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/bin/mklvars.sh intel64

source /opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpivars.sh intel64

然后 source ~/.bashrc

测试:

which ifort / which mpiifort 显示具体路径

Intel编译器套件安装完后，在任意目录下，执行：icc -v 显示版本号

然后进入$MKLROOT/interfaces/fftw3xf文件夹，执行：make libintel64 将会生成一个名为libfftw3xf_intel.a的静态库文件

在/etc/目录中新建一个名为mpd.conf的文本文件，在里面填写上(需root权限)：

MPD_SECRETWORD=mr45-j9z

然后保存退出，给这个文件加上权限：

chmod 600 /etc/mpd.conf

2. 安装libint (1.1.6版本)：

下载安装包解压，进入执行：

aclocal -I lib/autoconf

autoconf

注意，上面两个如果执行后都报错的话，不用管，直接下一步。

./configure –prefix=/opt/libint –with-ar=ar FC=ifort F77=ifort F90=ifort

FCFLAGS=”-O3 -xHost” CC=icc CFLAGS=”-O3 -xHost “ CXX=icpc

CXXFLAGS=”-O3 -xHost “ –with-cc-optflags=”-O3 -xHost “

–with-cxx-optflags=”-O3  -xHost “ –with-libint-max-am=5 –with-libint-opt-am=4 –with-libderiv-max-am1=4 –with-libderiv-max-am2=2 –with-libr12-max-am=2 –with-libr12-opt-am=2

make -j 8

make install

make realclean

3. 安装最新libxsmm (1.8.1的master版本，其他版本也行，用于矩阵运算加速的)：

解压安装包后，进入安装包，执行：

make CXX=icpc CC=icc FC=ifort AR=ar OPT=3 TARGET=”-xHost” ROW_MAJOR=0

INDICES_M=”$(echo $(seq 1 24))” INDICES_N=”$(echo $(seq 1 24))” INDICES_K=”$(echo $(seq 1 24))” PREFIX=/opt/libxsmm/ install

make clean

4. 安装libxc (3.0.0版本，其他版本也行)：

下载安装包解压进入安装：

./configure –prefix=/opt/libxc/ FC=ifort FCFLAGS=”-O3 -xHost “ CC=iccCFLAGS=”-O3 -xHost “

make -j 8

make install

make clean

5. 安装elpa :

cp2k 6.1.0-release版本目前采用elpa-2018.05.001

openmp版本(用于多线程多进程(psmp)版本：

./configure –prefix=/opt/elpa/ FC=mpiifort CC=mpiicc CXX=mpiicpc

CFLAGS=”-O3 -xHost “ CXXFLAGS=”-O3 -xHost “ FCFLAGS=”-O3 -xHost “

--with-avx-optimization=yes –enable-openmp SCALAPACK_LDFLAGS=”-

L$MKLROOT/lib/intel64 -lmkl_blas95_lp64 -lmkl_lapack95_lp64

-lmkl_scalapack_lp64 -Wl,–start-group -lmkl_cdft_core -lmkl_intel_lp64

-lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -Wl,–end-group

-liomp5 -lpthread -lm -ldl -Wl,-rpath,$MKLROOT/lib/intel64”

SCALAPACK_FCFLAGS=”-L$MKLROOT/lib/intel64 -lmkl_blas95_lp64 -lmkl_lapack95_lp64 -lmkl_scalapack_lp64 -lmkl_cdft_core -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lm -ldl -I$MKLROOT/include/intel64/lp64”

make

make install

make clean

6. 下载并安装cp2k：

下载6.1.0版本cp2k(development版本)：

手动进入网页下载：https://sourceforge.net/p/cp2k/code/HEAD/tree/

下载完成后，将trunk目录里面的cp2k/ 这个文件夹拷贝到/opt/目录中

然后进入/opt/cp2k/makefile目录，修改cp2k配置文件：

vim ../arch/Linux-x86-64-intel.psmp

然后对照着修改:

LIBXSMM  = /opt/libxsmm(对应各人安装路径)

LIBXC    = /opt/libxc

LIBINT   = /opt/libint

LIBELPA  = /opt/elpa

elpa部分的include后面部分要注意，每个版本的elpa此处数字路径是不一样的，具体路径请到elpa的安装目录自己查看

DFLAGS   = -D__ELPA=201805(elpa版本号)

FCFLAGS += -I$(LIBELPA)/include/elpa_openmp-2018.05.001/modules -I$(LIBELPA)/include/elpa_openmp-2018.05.001/elpa

保存文件,然后进入cp2k/makefils编译cp2k.psmp

cd cp2k/makefiles

多线程多进程版本

make -j 8 ARCH=Linux-x86-64-intel-host VERSION=psmp

使用多线程版本cp2k时，需要手动设置线程数：

export OMP_NUM_THREADS=2

然后再执行:

mpirun -n 14 cp2k.psmp -i test.inp

这样的命令，程序就会自动使用14核2线程,需要注意的是，核心数乘以线程数不能大于单节点上总的物理核心数，不然计算会非常慢！

0%
\ No newline at end of file +CP2K6.1 Install | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

CP2K6.1 Install

CP2K 6.1 编译安装 (Intel 编译器)

CP2K 6.1.0-release 多进程多线程(MPI+OPENMP)

制作者：曹立群

更新时间：2019.10.09

测试版本：CP2K 6.1.0-release

本文基于前辈安装老版本的说明撰写：

https://blog.csdn.net/zh314js/article/details/76258705

1.下载并安装intel编译器(最新版本2019)

安装后在~/.bashrc添加:

source /opt/intel/compilers_and_libraries_2017.4.196/linux/bin/ifortvars.sh intel64

source /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/bin/mklvars.sh intel64

source /opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpivars.sh intel64

然后 source ~/.bashrc

测试:

which ifort / which mpiifort 显示具体路径

Intel编译器套件安装完后，在任意目录下，执行：icc -v 显示版本号

然后进入$MKLROOT/interfaces/fftw3xf文件夹，执行：make libintel64 将会生成一个名为libfftw3xf_intel.a的静态库文件

在/etc/目录中新建一个名为mpd.conf的文本文件，在里面填写上(需root权限)：

MPD_SECRETWORD=mr45-j9z

然后保存退出，给这个文件加上权限：

chmod 600 /etc/mpd.conf

2. 安装libint (1.1.6版本)：

下载安装包解压，进入执行：

aclocal -I lib/autoconf

autoconf

注意，上面两个如果执行后都报错的话，不用管，直接下一步。

./configure –prefix=/opt/libint –with-ar=ar FC=ifort F77=ifort F90=ifort

FCFLAGS=”-O3 -xHost” CC=icc CFLAGS=”-O3 -xHost “ CXX=icpc

CXXFLAGS=”-O3 -xHost “ –with-cc-optflags=”-O3 -xHost “

–with-cxx-optflags=”-O3  -xHost “ –with-libint-max-am=5 –with-libint-opt-am=4 –with-libderiv-max-am1=4 –with-libderiv-max-am2=2 –with-libr12-max-am=2 –with-libr12-opt-am=2

make -j 8

make install

make realclean

3. 安装最新libxsmm (1.8.1的master版本，其他版本也行，用于矩阵运算加速的)：

解压安装包后，进入安装包，执行：

make CXX=icpc CC=icc FC=ifort AR=ar OPT=3 TARGET=”-xHost” ROW_MAJOR=0

INDICES_M=”$(echo $(seq 1 24))” INDICES_N=”$(echo $(seq 1 24))” INDICES_K=”$(echo $(seq 1 24))” PREFIX=/opt/libxsmm/ install

make clean

4. 安装libxc (3.0.0版本，其他版本也行)：

下载安装包解压进入安装：

./configure –prefix=/opt/libxc/ FC=ifort FCFLAGS=”-O3 -xHost “ CC=iccCFLAGS=”-O3 -xHost “

make -j 8

make install

make clean

5. 安装elpa :

cp2k 6.1.0-release版本目前采用elpa-2018.05.001

openmp版本(用于多线程多进程(psmp)版本：

./configure –prefix=/opt/elpa/ FC=mpiifort CC=mpiicc CXX=mpiicpc

CFLAGS=”-O3 -xHost “ CXXFLAGS=”-O3 -xHost “ FCFLAGS=”-O3 -xHost “

--with-avx-optimization=yes –enable-openmp SCALAPACK_LDFLAGS=”-

L$MKLROOT/lib/intel64 -lmkl_blas95_lp64 -lmkl_lapack95_lp64

-lmkl_scalapack_lp64 -Wl,–start-group -lmkl_cdft_core -lmkl_intel_lp64

-lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -Wl,–end-group

-liomp5 -lpthread -lm -ldl -Wl,-rpath,$MKLROOT/lib/intel64”

SCALAPACK_FCFLAGS=”-L$MKLROOT/lib/intel64 -lmkl_blas95_lp64 -lmkl_lapack95_lp64 -lmkl_scalapack_lp64 -lmkl_cdft_core -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lm -ldl -I$MKLROOT/include/intel64/lp64”

make

make install

make clean

6. 下载并安装cp2k：

下载6.1.0版本cp2k(development版本)：

手动进入网页下载：https://sourceforge.net/p/cp2k/code/HEAD/tree/

下载完成后，将trunk目录里面的cp2k/ 这个文件夹拷贝到/opt/目录中

然后进入/opt/cp2k/makefile目录，修改cp2k配置文件：

vim ../arch/Linux-x86-64-intel.psmp

然后对照着修改:

LIBXSMM  = /opt/libxsmm(对应各人安装路径)

LIBXC    = /opt/libxc

LIBINT   = /opt/libint

LIBELPA  = /opt/elpa

elpa部分的include后面部分要注意，每个版本的elpa此处数字路径是不一样的，具体路径请到elpa的安装目录自己查看

DFLAGS   = -D__ELPA=201805(elpa版本号)

FCFLAGS += -I$(LIBELPA)/include/elpa_openmp-2018.05.001/modules -I$(LIBELPA)/include/elpa_openmp-2018.05.001/elpa

保存文件,然后进入cp2k/makefils编译cp2k.psmp

cd cp2k/makefiles

多线程多进程版本

make -j 8 ARCH=Linux-x86-64-intel-host VERSION=psmp

使用多线程版本cp2k时，需要手动设置线程数：

export OMP_NUM_THREADS=2

然后再执行:

mpirun -n 14 cp2k.psmp -i test.inp

这样的命令，程序就会自动使用14核2线程,需要注意的是，核心数乘以线程数不能大于单节点上总的物理核心数，不然计算会非常慢！

0%
\ No newline at end of file diff --git a/group-seminar/index.html b/group-seminar/index.html index db2172680..fa6f19096 100644 --- a/group-seminar/index.html +++ b/group-seminar/index.html @@ -1 +1 @@ -Group Seminar | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Group Seminar

DateName
6月22日曹立群 & 左丰
7月6日张琪 & 方小牛
7月20日王博 & 曹立群
8月3日肖进 & 张琪
8月17日雷琪 & 汪晨
9月7日方小牛 & 王博
9月21日汪晨 & 肖进
10月12日陈泊锦 & 雷琪
10月26日黎娜 & 方小牛
11月9日左丰 & 黎娜
0%
\ No newline at end of file +Group Seminar | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Group Seminar

DateName
6月22日曹立群 & 左丰
7月6日张琪 & 方小牛
7月20日王博 & 曹立群
8月3日肖进 & 张琪
8月17日雷琪 & 汪晨
9月7日方小牛 & 王博
9月21日汪晨 & 肖进
10月12日陈泊锦 & 雷琪
10月26日黎娜 & 方小牛
11月9日左丰 & 黎娜
0%
\ No newline at end of file diff --git a/index.html b/index.html index 9cf0cbc14..46003afe1 100644 --- a/index.html +++ b/index.html @@ -1 +1 @@ -Tong Zhu Research Group - The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Posted on In
愿中国青年都摆脱冷气，只是向上走 不必听自暴自弃者流的话 能做事的做事，能发声的发声 有一分热，发一分光，就令萤火一般，也可以在黑暗里发一点光，不必等候炬火 此后如竟没有炬火：我便是唯一的光 倘若有了炬火，出了太阳，我们自然心悦诚服的消失 不但毫无不平，而且还要随喜赞美这炬火或太阳 因为他照了人类，连我都在内。

Posted on In

In the past two months, Yu and Jinzhe have got offers from the graduate school of Rice and Rutgers Universities (Ph.D. program), respectively. Cheers!

Best wishes as you begin following your dreams!!!

Posted on In

Congratulations to Mingyuan, out work on the fragment-based QM calculation of metalloproteins has been accepted by JCTC.

DOI: 10.1021/acs.jctc.8b00966

0%
\ No newline at end of file +Tong Zhu Research Group - The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Posted on In
愿中国青年都摆脱冷气，只是向上走 不必听自暴自弃者流的话 能做事的做事，能发声的发声 有一分热，发一分光，就令萤火一般，也可以在黑暗里发一点光，不必等候炬火 此后如竟没有炬火：我便是唯一的光 倘若有了炬火，出了太阳，我们自然心悦诚服的消失 不但毫无不平，而且还要随喜赞美这炬火或太阳 因为他照了人类，连我都在内。

Posted on In

In the past two months, Yu and Jinzhe have got offers from the graduate school of Rice and Rutgers Universities (Ph.D. program), respectively. Cheers!

Best wishes as you begin following your dreams!!!

Posted on In

Congratulations to Mingyuan, out work on the fragment-based QM calculation of metalloproteins has been accepted by JCTC.

DOI: 10.1021/acs.jctc.8b00966

0%
\ No newline at end of file diff --git a/memory/index.html b/memory/index.html index a054dd753..4fb670bb4 100644 --- a/memory/index.html +++ b/memory/index.html @@ -1 +1 @@ -Memory | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Memory

2019-04-20 Group meeting.

0%
\ No newline at end of file +Memory | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Memory

2019-04-20 Group meeting.

0%
\ No newline at end of file diff --git a/people/index.html b/people/index.html index f35e9de13..9aed582ad 100644 --- a/people/index.html +++ b/people/index.html @@ -1 +1 @@ -Team | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Team

1UZOmNVE8C3GgIQEWpj7qmzCb5v63VXK5

Tong Zhu 朱通

A1008, Tower A, Science Building
School of Chemistry and Molecular Engineering
East China Normal University
物理化学专业，化学与分子工程学院，华东师范大学
NYU-ECNU Center for Computational Chemistry at NYU Shanghai

tzhu#lps.ecnu.edu.cn  tongzhu.work#gmail.com         
021-62235445
https://faculty.ecnu.edu.cn/_s34/zt2/main.psp

Chih-Hao Chin, 金之豪

RM 1006, Tower A, Science Building
School of Chemistry and Molecular Engineering
East China Normal University
NYU-ECNU Center for Computational Chemistry at NYU Shanghai

1NiNWaefiGycXikb5xKJch0rlTk2S6L1j

Mingyuan Xu (徐明远)

Liqun Cao (曹立群)

1hnl6DMFNxJjaXadizrYyavk2-o7BgXl0

Zhenmei Gao (高振梅)

1EJbd2t8oQKQD6zvOwaN_eCehLkP-WGQr

Yao Liu (刘瑶)

1PHwNY3XzWih0TvM4LU9of620a9G4rpAv

Jin Xiao (肖进)

1olRKzsFVDTjC5M3EDkofDiklkDx1HsZ7

Qi Zhang (张琪)

1YD5HsrIWTLWSCLKk6dIWh-PNzCxjJg1v

Qi Lei (雷琪)

1PbwAR-9Vu3S9gzzXZ_oF9EUNK4DXplxt

Na Li (黎娜)

1-k9x2cTJXBlmx2YkKvJb1uvFNHA0pg1s

Shuangfei Gu (顾双菲)

1KTxISSyr9VyWd5zspFgsmKfRwxpkSeVQ

Qiang Shen (沈强)

1QKN5C4DUVSH0WaEjPQFEfaLh7I6lEfyg

Jiale Wang (王佳乐)

Alumni

1lPe7mOxM8PHJAEvld7uuF4J_dkTSt1c3

Pei Zhao (赵培): 2016-2019, 硕士研究生, 国家知识产权专利局

1KTxISSyr9VyWd5zspFgsmKfRwxpkSeVQ

Huali Cao (曹华丽): 2016-2019, 硕士研究生, 上海市静安实验中学

1suV2jdlRhn3GueBa3mpDfesU2T17UVN2

Jinzhe Zeng (曾晋哲): 2017-2019, 本科生, Rutgers University

Yu Cheng (陈娱): 2018-2019, 本科生, Rice Univerisity

Yanping Yang (杨颜萍): 2018-2019, 本科生，龙岩中学

Graduate student positions are always available!!!

0%
\ No newline at end of file +Team | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Team

1UZOmNVE8C3GgIQEWpj7qmzCb5v63VXK5

Tong Zhu 朱通

A1008, Tower A, Science Building
School of Chemistry and Molecular Engineering
East China Normal University
物理化学专业，化学与分子工程学院，华东师范大学
NYU-ECNU Center for Computational Chemistry at NYU Shanghai

tzhu#lps.ecnu.edu.cn  tongzhu.work#gmail.com         
021-62235445
https://faculty.ecnu.edu.cn/_s34/zt2/main.psp

Chih-Hao Chin, 金之豪

RM 1006, Tower A, Science Building
School of Chemistry and Molecular Engineering
East China Normal University
NYU-ECNU Center for Computational Chemistry at NYU Shanghai

1NiNWaefiGycXikb5xKJch0rlTk2S6L1j

Mingyuan Xu (徐明远)

Liqun Cao (曹立群)

1hnl6DMFNxJjaXadizrYyavk2-o7BgXl0

Zhenmei Gao (高振梅)

1EJbd2t8oQKQD6zvOwaN_eCehLkP-WGQr

Yao Liu (刘瑶)

1PHwNY3XzWih0TvM4LU9of620a9G4rpAv

Jin Xiao (肖进)

1olRKzsFVDTjC5M3EDkofDiklkDx1HsZ7

Qi Zhang (张琪)

1YD5HsrIWTLWSCLKk6dIWh-PNzCxjJg1v

Qi Lei (雷琪)

1PbwAR-9Vu3S9gzzXZ_oF9EUNK4DXplxt

Na Li (黎娜)

1-k9x2cTJXBlmx2YkKvJb1uvFNHA0pg1s

Shuangfei Gu (顾双菲)

1KTxISSyr9VyWd5zspFgsmKfRwxpkSeVQ

Qiang Shen (沈强)

1QKN5C4DUVSH0WaEjPQFEfaLh7I6lEfyg

Jiale Wang (王佳乐)

Alumni

1lPe7mOxM8PHJAEvld7uuF4J_dkTSt1c3

Pei Zhao (赵培): 2016-2019, 硕士研究生, 国家知识产权专利局

1KTxISSyr9VyWd5zspFgsmKfRwxpkSeVQ

Huali Cao (曹华丽): 2016-2019, 硕士研究生, 上海市静安实验中学

1suV2jdlRhn3GueBa3mpDfesU2T17UVN2

Jinzhe Zeng (曾晋哲): 2017-2019, 本科生, Rutgers University

Yu Cheng (陈娱): 2018-2019, 本科生, Rice Univerisity

Yanping Yang (杨颜萍): 2018-2019, 本科生，龙岩中学

Graduate student positions are always available!!!

0%
\ No newline at end of file diff --git a/publications/index.html b/publications/index.html index a14c8d81d..50d30c526 100644 --- a/publications/index.html +++ b/publications/index.html @@ -1 +1 @@ -Publications | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Publications

2021

Fragment-based Ab Initio Molecular Dynamics Simulation for Combustion

Liqun Cao, Jinzhe Zeng, Mingyuan Xu, Chih-Hao Chin, Tong Zhu, John ZH Zhang
Molecules, 2021, 26 (11), 3120.
DOI: 10.3390/molecules26113120

Cyclopentadienyl radical formation from the reaction of excited nitrogen atoms with benzene: A theoretical study

Chih-Hao Chin, Tong Zhu, John ZH Zhang
Physical Chemistry Chemical Physics, 2021.
DOI: 10.1039/D1CP00133G

Automatically Construct Neural Network Potentials for Molecular Dynamics Simulation of Zinc Proteins

Mingyuan Xu, Tong Zhu, John ZH Zhang
Frontiers in Chemistry, 2021, 9, 385.
DOI: 10.3389/fchem.2021.692200

Extensive Evaluation of Force Fields for G-Quadruplexes

Na Li, Tong Zhu
ChemRxiv Preprint.
DOI: 10.26434/chemrxiv.14369897

Binding Mechanisms of fluorophores to Mango-II revealed by multiple-replica molecular dynamics simulations

Junxiao Chen, Na Li, Xingyu Wang, Jianzhong Chen, John ZH Zhang, Tong Zhu
Physical Chemistry Chemical Physics, 2021.
DOI: 10.1039/D0CP06438F

Engineering the biomimetic cofactors of NMNH for cytochrome P450 BM3 based on binding conformation refinement

Yao Liu, Yalong Cong, Chuanxi Zhang, Bohuan Fang, Yue Pan, Qiangzi Li, Chun You, Bei Gao, John ZH Zhang, Tong Zhu, Lujia Zhang
RSC Advances, 2021, 11 (20), 12036–12042.
DOI: 10.1039/D1RA00352F

Exploring the Chemical Space of Linear Alkane Pyrolysis via Deep Potential GENerator

Jinzhe Zeng, Linfeng Zhang, Han Wang, Tong Zhu
Energy & Fuels, 2021, 35 (1), 762–769.
DOI: 10.1021/acs.energyfuels.0c03211

2020

Pharmacological activation of the p53 pathway by a new compound CYZ2017 exerts anti-tumor effects

Yuqiao Han, Ziwei Ren, Yixin Wu, Yunzhong Chen, Zhenmei Cui, Tong Zhu, Mingliang Ma, Yijie Du, Suzhen Dong
Biochemical and Biophysical Research Communications, 2020, 533 (4), 1069–1075.
DOI: 10.1016/j.bbrc.2020.09.122

Ab Initio Molecular Dynamics Simulation of Zinc metalloproteins with Enhanced Self-Organizing Incremental High Dimensional Neural Network

Mingyuan Xu, Tong Zhu, John ZH Zhang
ChemRxiv, 2020.
DOI: 10.26434/chemrxiv.13207967

Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation

Jinzhe Zeng, Liqun Cao, Mingyuan Xu, Tong Zhu, John ZH Zhang
Nature communications, 2020, 11 (1), 1–9.
DOI: 10.1038/s41467-020-19497-z

Design, synthesis, and structure activity relationship (SAR) studies of novel imidazo [1, 2-a] pyridine derivatives as Nek2 inhibitors

Haili Wang, Yunzhong Chen, Xiaofan Gu, Jianbei Xi, Ziwei Ren, Shuting Wang, Yanhong Duan, Hongyu Li, Tong Zhu, Yijie Du, Xiongwen Zhang, Mingliang Ma
Bioorganic & Medicinal Chemistry, 2020, 28 (23), 115775.
DOI: 10.1016/j.bmc.2020.115775

An Approach to Computing Solvent Reorganization Energy

Bo Wang, Cuiyu Li, Jia Xiangyu, Tong Zhu, John ZH Zhang
Journal of Chemical Theory and Computation, 2020, 16 (10), 6513–6519.
DOI: 10.1021/acs.jctc.0c00672

Reaction mechanism and product branching ratios of $\ce{OH + C2H3F}$ reaction: A theoretical study

Chih-Hao Chin, Tong Zhu, John Zeng-Hui Zhang
Chinese Journal of Chemical Physics, 2020, 33 (2), 203–209.
DOI: 10.1063/1674-0068/cjcp2001016

An ab initio/RRKM study of the reaction mechanism and product branching ratios of $\ce{CH3OH+}$ and $\ce{CH3OH++}$ dissociation

Cuiyu Li, Chih-Hao Chin, Tong Zhu, John Zeng Hui Zhang
Journal of Molecular Structure, 2020, 1217, 128410.
DOI: 10.1016/j.molstruc.2020.128410

Effect of mutations on drug resistance of smoothened receptor toward inhibitors probed by molecular modeling

Zhenmei Gao, Jingxiao Bao, Shuhua Shi, Xiongwen Zhang, Ya Gao, Tong Zhu
Chemical Physics Letters, 2020, 741, 137126.
DOI: 10.1016/j.cplett.2020.137126

Supramolecular prodrug nanovectors for active tumor targeting and combination immunotherapy of colorectal cancer

Xianli Hu, Bo Hou, Zhiai Xu, Madiha Saeed, Fang Sun, Zhenmei Gao, Yi Lai, Tong Zhu, Fan Zhang, Wen Zhang, Huaijun Yu
Advanced Science, 2020, 7 (8), 1903332.
DOI: 10.1002/advs.201903332

ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamics simulations

Jinzhe Zeng, Liqun Cao, Chih-Hao Chin, Haisheng Ren, John ZH Zhang, Tong Zhu
Physical Chemistry Chemical Physics, 2020, 22 (2), 683–691.
DOI: 10.1039/C9CP05091D

2019

Formation mechanism and spectroscopy of $\ce{C6H}$ radicals in extreme environments: a theoretical study

Chih-Hao Chin, Tong Zhu, John Zeng Hui Zhang
Physical Chemistry Chemical Physics, 2019, 21 (41), 23044–23055.
DOI: 10.1039/C9CP03662H

Nanoporous $\ce{Ni3P}$ Evolutionarily Structured onto a Ni Foam for Highly Selective Hydrogenation of Dimethyl Oxalate to Methyl Glycolate

Jian Zhu, Liqun Cao, Cuiyu Li, Guofeng Zhao, Tong Zhu, Wei Hu, Weidong Sun, Yong Lu
ACS applied materials & interfaces, 2019, 11 (41), 37635–37643.
DOI: 10.1021/acsami.9b11703

Understanding the selectivity of inhibitors toward PI4KIII$\alpha$ and PI4KIII$\beta$ based molecular modeling

Shuaizhen Tian, Jinzhe Zeng, Xiao Liu, Jianzhong Chen, John ZH Zhang, Tong Zhu
Physical Chemistry Chemical Physics, 2019, 21 (39), 22103–22112.
DOI: 10.1039/C9CP03598B

Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologies

Jianzhong Chen, Baohua Yin, Laixue Pang, Wei Wang, John ZH Zhang, Tong Zhu
Journal of Biomolecular Structure and Dynamics, 2019.
DOI: 10.1080/07391102.2019.1624616

Molecular Dynamics Simulation of Zinc Ion in Water with an ab Initio Based Neural Network Potential

Mingyuan Xu, Tong Zhu, John ZH Zhang
The Journal of Physical Chemistry A, 2019, 123 (30), 6587–6595.
DOI: 10.1021/acs.jpca.9b04087

Self-assembly of metallo-nucleoside hydrogels for injectable materials that promote wound closure

Qian Tang, Taylor N Plank, Tong Zhu, Huizhen Yu, Zhilei Ge, Qian Li, Li Li, Jeffery T Davis, Hao Pei
ACS applied materials & interfaces, 2019, 11 (22), 19743–19750.
DOI: 10.1021/acsami.9b02265

Comparison of RP-3 pyrolysis reactions between surrogates and 45-component model by ReaxFF molecular dynamics simulations

Pei Zhao, Song Han, Xiaoxia Li, Tong Zhu, Xiaofang Tao, Li Guo
Energy & Fuels, 2019, 33 (8), 7176–7187.
DOI: 10.1021/acs.energyfuels.9b01321

Understanding Aldose Reductase-Inhibitors interactions with free energy simulation

Zhaoxi Sun, Xiaohui Wang, Qianqian Zhao, Tong Zhu
Journal of Molecular Graphics and Modelling, 2019, 91, 10–21.
DOI: 10.1016/j.jmgm.2019.05.011

Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations

Jianzhong Chen, Xingyu Wang, Laixue Pang, John ZH Zhang, Tong Zhu
Nucleic acids research, 2019, 47 (13), 6618–6631.
DOI: 10.1093/nar/gkz499

Insights into the binding mechanisms of inhibitors of MDM2 based on molecular dynamics simulations and binding free energy calculations

Pei Zhao, Huali Cao, Yu Chen, Tong Zhu
Chemical Physics Letters, 2019, 728, 94–101.
DOI: 10.1016/j.cplett.2019.05.001

Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations

Jianzhong Chen, Laixue Pang, Wei Wang, Lifei Wang, John ZH Zhang, Tong Zhu
Journal of Biomolecular Structure and Dynamics, 2019.
DOI: 10.1080/07391102.2019.1591304

L-4, a well-tolerated and orally active inhibitor of Hedgehog pathway, exhibited potent anti-tumor effects against medulloblastoma in vitro and in vivo

Mingfei Zhu, Hong Wang, Chenglin Wang, Yanfen Fang, Tong Zhu, Weili Zhao, Xiaochun Dong, Xiongwen Zhang
Frontiers in pharmacology, 2019, 10, 89.
DOI: 10.3389/fphar.2019.00089

A fragment quantum mechanical method for metalloproteins

Mingyuan Xu, Xiao He, Tong Zhu, John ZH Zhang
Journal of chemical theory and computation, 2019, 15 (2), 1430–1439.
DOI: 10.1021/acs.jctc.8b00966

2018

Effect of substituents in different positions of aminothiazole hinge-binding scaffolds on inhibitor--CDK2 association probed by interaction entropy method

Jianzhong Chen, Xingyu Wang, John ZH Zhang, Tong Zhu
ACS Omega, 2018, 3 (12), 18052–18064.
DOI: 10.1021/acsomega.8b02354

Comparison of the unfolding and oligomerization of human prion protein under acidic and neutral environments by molecular dynamics simulations

Ya Gao, Tong Zhu, Chaomin Zhang, John ZH Zhang, Ye Mei
Chemical Physics Letters, 2018, 706, 594–600.
DOI: 10.1016/j.cplett.2018.07.014

Exploring drug-resistant mechanisms of I84V mutation in HIV-1 protease toward different inhibitors by thermodynamics integration and solvated interaction energy method

Ya Gao, Tong Zhu, Jianzhong Chen
Chemical Physics Letters, 2018, 706, 400–408.
DOI: 10.1016/j.cplett.2018.06.040

Donor engineering for NIR-II molecular fluorophores with enhanced fluorescent performance

Qinglai Yang, Zhubin Hu, Shoujun Zhu, Rui Ma, Huilong Ma, Zhuoran Ma, Hao Wan, Tong Zhu, Zhengyan Jiang, Weiqiang Liu, Liying Jiao, Haitao Sun, Yongye Liang, Hongjie Dai
Journal of the American Chemical Society, 2018, 140 (5), 1715–1724.
DOI: 10.1021/jacs.7b10334

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein

Mingyuan Xu, Tong Zhu, John ZH Zhang
Frontiers in chemistry, 2018, 6, 189.
DOI: 10.3389/fchem.2018.00189

A quantum mechanical computational method for modeling electrostatic and solvation effects of protein

Xianwei Wang, Yang Li, Ya Gao, Zejin Yang, Chenhui Lu, Tong Zhu
Scientific reports, 2018, 8 (1), 1–10.
DOI: 10.1038/s41598-018-23783-8

Automated fragmentation QM/MM calculation of NMR chemical shifts for protein-ligand complexes

Xinsheng Jin, Tong Zhu, John ZH Zhang, Xiao He
Frontiers in chemistry, 2018, 6, 150.
DOI: 10.3389/fchem.2018.00150

2017

Structure-based design and synthesis of imidazo [1, 2-a] pyridine derivatives as novel and potent Nek2 inhibitors with in vitro and in vivo antitumor activities

Jian-Bei Xi, Yan-Fen Fang, Brendan Frett, Meng-Li Zhu, Tong Zhu, Yan-Nan Kong, Feng-Jie Guan, Yun Zhao, Xiong-Wen Zhang, Hong-Yu Li, Ming-Liang Ma, Wenhao Hu
European journal of medicinal chemistry, 2017, 126, 1083–1106.
DOI: 10.1016/j.ejmech.2016.12.026

Optimization of convergence criteria for fragmentation methods

Zhaoxi Sun, Tong Zhu, Xiaohui Wang, Ye Mei, John ZH Zhang
Chemical Physics Letters, 2017, 687, 163–170.
DOI: 10.1016/j.cplett.2017.08.059

Origins of Protons in C--H Bond Insertion Products of Phenols: Proton-Self-Sufficient Function via Water Molecules

Zhoujie Luo, Ya Gao, Tong Zhu, John Zenghui Zhang, Fei Xia
The Journal of Physical Chemistry A, 2017, 121 (34), 6523–6529.
DOI: 10.1021/acs.jpca.7b06411

An electrochemical biosensor with dual signal outputs: toward simultaneous quantification of pH and $\ce{O2}$ in the brain upon ischemia and in a tumor during cancer starvation therapy

Li Liu, Fan Zhao, Wei Liu, Tong Zhu, John ZH Zhang, Chen Chen, Zhihui Dai, Huisheng Peng, Jun-Long Huang, Qin Hu, Wenbo Bu, Yang Tian
Angewandte Chemie International Edition, 2017, 56 (35), 10471–10475.
DOI: 10.1002/anie.201705615

Single biosensor for simultaneous quantification of glucose and pH in a rat brain of diabetic model using both current and potential outputs

Shuai Li, Anwei Zhu, Tong Zhu, John ZH Zhang, Yang Tian
Analytical chemistry, 2017, 89 (12), 6656–6662.
DOI: 10.1021/acs.analchem.7b00881

Discovery of Bisindole as a Novel Scaffold for Protein Tyrosine Phosphatase 1B Inhibitors

Changcheng Jing, Ziyan Li, Kaili Jia, Chen Chen, Xiao Liu, Beibei Wang, Wenhao Hu, Jia Li, Tong Zhu, Suzhen Dong
Archiv der Pharmazie, 2017, 350 (1), e1600173.
DOI: 10.1002/ardp.201600173

A theoretical study of the substituent effect on reactions of amines, carbon dioxide and ethylene oxide catalyzed by binary ionic liquids

Minmin Huang, Zhoujie Luo, Tong Zhu, Jian Chen, John Zenghui Zhang, Fei Xia
RSC advances, 2017, 7 (81), 51521–51527.
DOI: 10.1039/C7RA09485J

A test of AMBER force fields in predicting the secondary structure of $\alpha$-helical and $\beta$-hairpin peptides

Ya Gao, Chaomin Zhang, Xianwei Wang, Tong Zhu
Chemical Physics Letters, 2017, 679, 112–118.
DOI: 10.1016/j.cplett.2017.04.074

Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations

Li L Duan, T Zhu, Yu C Li, Qing G Zhang, John ZH Zhang
Scientific reports, 2017, 7 (1), 1–14.
DOI: 10.1038/srep42223

Direct folding simulation of helical proteins using an effective polarizable bond force field

Lili Duan, Tong Zhu, Changge Ji, Qinggang Zhang, John ZH Zhang
Physical Chemistry Chemical Physics, 2017, 19 (23), 15273–15284.
DOI: 10.1039/C7CP02101A

Discovery of core-structurally novel PTP1B inhibitors with specific selectivity containing oxindole-fused spirotetrahydrofurochroman by one-pot reaction

Suzhen Dong, Yubing Lei, Shikun Jia, Lixin Gao, Jia Li, Tong Zhu, Shunying Liu, Wenhao Hu
Bioorganic & medicinal chemistry letters, 2017, 27 (4), 1105–1108.
DOI: 10.1016/j.bmcl.2016.11.055

2016

Predicted PAR1 inhibitors from multiple computational methods

Ying Wang, Jinfeng Liu, Tong Zhu, Lujia Zhang, Xiao He, John ZH Zhang
Chemical Physics Letters, 2016, 659, 295–303.
DOI: 10.1016/j.cplett.2016.07.059

New peptide deformylase inhibitors design, synthesis and pharmacokinetic assessment

Fengping Lv, Chen Chen, Yang Tang, Jianhai Wei, Tong Zhu, Wenhao Hu
Bioorganic & medicinal chemistry letters, 2016, 26 (15), 3714–3718.
DOI: 10.1016/j.bmcl.2016.05.077

PBSA_E: A PBSA-Based Free Energy Estimator for Protein--Ligand Binding Affinity

Xiao Liu, Jinfeng Liu, Tong Zhu, Lujia Zhang, Xiao He, John ZH Zhang
Journal of chemical information and modeling, 2016, 56 (5), 854–861.
DOI: 10.1021/acs.jcim.6b00001

Antitumor activity of TY-011 against gastric cancer by inhibiting Aurora A, Aurora B and VEGFR2 kinases

Wang Liu, Yu Lu, Xiaoping Chai, Xiao Liu, Tong Zhu, Xihan Wu, Yanfen Fang, Xuan Liu, Xiongwen Zhang
Journal of Experimental & Clinical Cancer Research, 2016, 35 (1), 1–15.
DOI: 10.1186/s13046-016-0464-2

A systematic study on RNA NMR chemical shift calculation based on the automated fragmentation QM/MM approach

Xinsheng Jin, Tong Zhu, John ZH Zhang, Xiao He
RSC advances, 2016, 6 (110), 108590–108602.
DOI: 10.1039/C6RA22518G

Preclinical activity of MBM-5 in gastrointestinal cancer by inhibiting NEK2 kinase activity

Yanfen Fang, Yannan Kong, Jianbei Xi, Mengli Zhu, Tong Zhu, Tongtong Jiang, Brendan Frett, Wenhao Hu, Hong-yu Li, Mingliang Ma, others
Oncotarget, 2016, 7 (48), 79327.
DOI: 10.18632/oncotarget.12687

2015

Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method

Tong Zhu, John ZH Zhang, Xiao He
Advance in Structural Bioinformatics, 2015, 49–70.
DOI: 10.1007/978-94-017-9245-5_5

AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules

Jason Swails, Tong Zhu, Xiao He, David A Case
Journal of biomolecular NMR, 2015, 63 (2), 125–139.
DOI: 10.1007/s10858-015-9970-3

A Comparative Insight into Amprenavir Resistance of Mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 Protease Based on Thermodynamic Integration and MM-PBSA Methods

Jianzhong Chen, Xingyu Wang, Tong Zhu, Qinggang Zhang, John ZH Zhang
Journal of chemical information and modeling, 2015, 55 (9), 1903–1913.
DOI: 10.1021/acs.jcim.5b00173

2010-2014

Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations

Tong Zhu, John ZH Zhang, Xiao He
Physical Chemistry Chemical Physics, 2014, 16 (34), 18163–18169.
DOI: 10.1039/C4CP02553A

Fragment Quantum Mechanical Calculation of Proteins and Its Applications

Xiao He, Tong Zhu, Xianwei Wang, Jinfeng Liu, John ZH Zhang
Accounts of chemical research, 2014, 47 (9), 2748–2757.
DOI: 10.1021/ar500077t

Electronic polarization stabilizes tertiary structure prediction of HP-36

Li L Duan, Tong Zhu, Qing G Zhang, Bo Tang, John ZH Zhang
Journal of molecular modeling, 2014, 20 (4), 1–19.
DOI: 10.1007/s00894-014-2195-7

Asp120Asn mutation impairs the catalytic activity of NDM-1 metallo-$\beta$-lactamase: experimental and computational study

Jiao Chen, Hui Chen, Tong Zhu, Dandan Zhou, Fang Zhang, Xingzhen Lao, Heng Zheng
Physical Chemistry Chemical Physics, 2014, 16 (14), 6709–6716.
DOI: 10.1039/C3CP55069A

Automated fragmentation QM/MM calculation of amide proton chemical shifts in proteins with explicit solvent model

Tong Zhu, John ZH Zhang, Xiao He
Journal of chemical theory and computation, 2013, 9 (4), 2104–2114.
DOI: 10.1021/ct300999w

A New Quantum Calibrated Force Field for Zinc–Protein Complex

Tong Zhu, Xudong Xiao, Changge Ji, John ZH Zhang
Journal of chemical theory and computation, 2013, 9 (3), 1788–1798.
DOI: 10.1021/ct301091z

An implementation of hydrophobic force in implicit solvent molecular dynamics simulation for packed proteins

Li L Duan, Tong Zhu, Ye Mei, Qing G Zhang, Bo Tang, John ZH Zhang
Journal of molecular modeling, 2013, 19 (6), 2605–2612.
DOI: 10.1007/s00894-013-1798-8

Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation

Tong Zhu, Xiao He, John ZH Zhang
Physical Chemistry Chemical Physics, 2012, 14 (21), 7837–7845.
DOI: 10.1039/C2CP23746F

Quasi-classical Trajectory Study of Reaction $\ce{O (^3P) + HCl (v= 2; j= 1, 6, 9) -> OH + Cl}$

Tong Zhu, Guo-Dong Hu, Qing-Gang Zhang
Chinese Physics Letters, 2010, 27 (3), 033102.
DOI: 10.1088/0256-307X/27/3/033102

Theoretical study of stereodynamics for reaction $\ce{O (^3P) + HCl}$

Tong Zhu, Guo-Dong Hu, Jian-Zhong Chen, Xin-Guo Liu, Qing-Gang Zhang
Chinese Physics B, 2010, 19 (8), 083402.
DOI: 10.1088/1674-1056/19/8/083402

Quasi-classical trajectory study of the reaction $\ce{O (^3P) + HCl -> OH + Cl}$ and $\ce{O (^3P) + DCl -> OD + Cl}$: Vector and scalar properties

Tong Zhu, Guodong Hu, Qinggang Zhang
Journal of Molecular Structure: THEOCHEM, 2010, 948 (1-3), 36–42.
DOI: 10.1016/j.theochem.2010.02.015

THE EFFECT OF VIBRATIONAL EXCITATION OF THE REACTION $\ce{O (^3 P) + HCl -> OH + Cl}$ FOR THE $^3 A^{″}$ ELECTRONIC STATES

Huirong Liu, Xinguo Liu, Tong Zhu, Haizhu Sun, Qinggang Zhang
Journal of Theoretical and Computational Chemistry, 2010, 9 (06), 1033–1042.
DOI: 10.1142/S0219633610006183

Some insights into mechanism for binding and drug resistance of wild type and I50V V82A and I84V mutations in HIV-1 protease with GRL-98065 inhibitor from molecular dynamic simulations

Guo-Dong Hu, Tong Zhu, Shao-Long Zhang, Dunyou Wang, Qing-Gang Zhang
European journal of medicinal chemistry, 2010, 45 (1), 227–235.
DOI: 10.1016/j.ejmech.2009.09.048

0%
\ No newline at end of file +Publications | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Publications

2021

Fragment-based Ab Initio Molecular Dynamics Simulation for Combustion

Liqun Cao, Jinzhe Zeng, Mingyuan Xu, Chih-Hao Chin, Tong Zhu, John ZH Zhang
Molecules, 2021, 26 (11), 3120.
DOI: 10.3390/molecules26113120

Cyclopentadienyl radical formation from the reaction of excited nitrogen atoms with benzene: A theoretical study

Chih-Hao Chin, Tong Zhu, John ZH Zhang
Physical Chemistry Chemical Physics, 2021.
DOI: 10.1039/D1CP00133G

Automatically Construct Neural Network Potentials for Molecular Dynamics Simulation of Zinc Proteins

Mingyuan Xu, Tong Zhu, John ZH Zhang
Frontiers in Chemistry, 2021, 9, 385.
DOI: 10.3389/fchem.2021.692200

Extensive Evaluation of Force Fields for G-Quadruplexes

Na Li, Tong Zhu
ChemRxiv Preprint.
DOI: 10.26434/chemrxiv.14369897

Binding Mechanisms of fluorophores to Mango-II revealed by multiple-replica molecular dynamics simulations

Junxiao Chen, Na Li, Xingyu Wang, Jianzhong Chen, John ZH Zhang, Tong Zhu
Physical Chemistry Chemical Physics, 2021.
DOI: 10.1039/D0CP06438F

Engineering the biomimetic cofactors of NMNH for cytochrome P450 BM3 based on binding conformation refinement

Yao Liu, Yalong Cong, Chuanxi Zhang, Bohuan Fang, Yue Pan, Qiangzi Li, Chun You, Bei Gao, John ZH Zhang, Tong Zhu, Lujia Zhang
RSC Advances, 2021, 11 (20), 12036–12042.
DOI: 10.1039/D1RA00352F

Exploring the Chemical Space of Linear Alkane Pyrolysis via Deep Potential GENerator

Jinzhe Zeng, Linfeng Zhang, Han Wang, Tong Zhu
Energy & Fuels, 2021, 35 (1), 762–769.
DOI: 10.1021/acs.energyfuels.0c03211

2020

Pharmacological activation of the p53 pathway by a new compound CYZ2017 exerts anti-tumor effects

Yuqiao Han, Ziwei Ren, Yixin Wu, Yunzhong Chen, Zhenmei Cui, Tong Zhu, Mingliang Ma, Yijie Du, Suzhen Dong
Biochemical and Biophysical Research Communications, 2020, 533 (4), 1069–1075.
DOI: 10.1016/j.bbrc.2020.09.122

Ab Initio Molecular Dynamics Simulation of Zinc metalloproteins with Enhanced Self-Organizing Incremental High Dimensional Neural Network

Mingyuan Xu, Tong Zhu, John ZH Zhang
ChemRxiv, 2020.
DOI: 10.26434/chemrxiv.13207967

Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation

Jinzhe Zeng, Liqun Cao, Mingyuan Xu, Tong Zhu, John ZH Zhang
Nature communications, 2020, 11 (1), 1–9.
DOI: 10.1038/s41467-020-19497-z

Design, synthesis, and structure activity relationship (SAR) studies of novel imidazo [1, 2-a] pyridine derivatives as Nek2 inhibitors

Haili Wang, Yunzhong Chen, Xiaofan Gu, Jianbei Xi, Ziwei Ren, Shuting Wang, Yanhong Duan, Hongyu Li, Tong Zhu, Yijie Du, Xiongwen Zhang, Mingliang Ma
Bioorganic & Medicinal Chemistry, 2020, 28 (23), 115775.
DOI: 10.1016/j.bmc.2020.115775

An Approach to Computing Solvent Reorganization Energy

Bo Wang, Cuiyu Li, Jia Xiangyu, Tong Zhu, John ZH Zhang
Journal of Chemical Theory and Computation, 2020, 16 (10), 6513–6519.
DOI: 10.1021/acs.jctc.0c00672

Reaction mechanism and product branching ratios of $\ce{OH + C2H3F}$ reaction: A theoretical study

Chih-Hao Chin, Tong Zhu, John Zeng-Hui Zhang
Chinese Journal of Chemical Physics, 2020, 33 (2), 203–209.
DOI: 10.1063/1674-0068/cjcp2001016

An ab initio/RRKM study of the reaction mechanism and product branching ratios of $\ce{CH3OH+}$ and $\ce{CH3OH++}$ dissociation

Cuiyu Li, Chih-Hao Chin, Tong Zhu, John Zeng Hui Zhang
Journal of Molecular Structure, 2020, 1217, 128410.
DOI: 10.1016/j.molstruc.2020.128410

Effect of mutations on drug resistance of smoothened receptor toward inhibitors probed by molecular modeling

Zhenmei Gao, Jingxiao Bao, Shuhua Shi, Xiongwen Zhang, Ya Gao, Tong Zhu
Chemical Physics Letters, 2020, 741, 137126.
DOI: 10.1016/j.cplett.2020.137126

Supramolecular prodrug nanovectors for active tumor targeting and combination immunotherapy of colorectal cancer

Xianli Hu, Bo Hou, Zhiai Xu, Madiha Saeed, Fang Sun, Zhenmei Gao, Yi Lai, Tong Zhu, Fan Zhang, Wen Zhang, Huaijun Yu
Advanced Science, 2020, 7 (8), 1903332.
DOI: 10.1002/advs.201903332

ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamics simulations

Jinzhe Zeng, Liqun Cao, Chih-Hao Chin, Haisheng Ren, John ZH Zhang, Tong Zhu
Physical Chemistry Chemical Physics, 2020, 22 (2), 683–691.
DOI: 10.1039/C9CP05091D

2019

Formation mechanism and spectroscopy of $\ce{C6H}$ radicals in extreme environments: a theoretical study

Chih-Hao Chin, Tong Zhu, John Zeng Hui Zhang
Physical Chemistry Chemical Physics, 2019, 21 (41), 23044–23055.
DOI: 10.1039/C9CP03662H

Nanoporous $\ce{Ni3P}$ Evolutionarily Structured onto a Ni Foam for Highly Selective Hydrogenation of Dimethyl Oxalate to Methyl Glycolate

Jian Zhu, Liqun Cao, Cuiyu Li, Guofeng Zhao, Tong Zhu, Wei Hu, Weidong Sun, Yong Lu
ACS applied materials & interfaces, 2019, 11 (41), 37635–37643.
DOI: 10.1021/acsami.9b11703

Understanding the selectivity of inhibitors toward PI4KIII$\alpha$ and PI4KIII$\beta$ based molecular modeling

Shuaizhen Tian, Jinzhe Zeng, Xiao Liu, Jianzhong Chen, John ZH Zhang, Tong Zhu
Physical Chemistry Chemical Physics, 2019, 21 (39), 22103–22112.
DOI: 10.1039/C9CP03598B

Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologies

Jianzhong Chen, Baohua Yin, Laixue Pang, Wei Wang, John ZH Zhang, Tong Zhu
Journal of Biomolecular Structure and Dynamics, 2019.
DOI: 10.1080/07391102.2019.1624616

Molecular Dynamics Simulation of Zinc Ion in Water with an ab Initio Based Neural Network Potential

Mingyuan Xu, Tong Zhu, John ZH Zhang
The Journal of Physical Chemistry A, 2019, 123 (30), 6587–6595.
DOI: 10.1021/acs.jpca.9b04087

Self-assembly of metallo-nucleoside hydrogels for injectable materials that promote wound closure

Qian Tang, Taylor N Plank, Tong Zhu, Huizhen Yu, Zhilei Ge, Qian Li, Li Li, Jeffery T Davis, Hao Pei
ACS applied materials & interfaces, 2019, 11 (22), 19743–19750.
DOI: 10.1021/acsami.9b02265

Comparison of RP-3 pyrolysis reactions between surrogates and 45-component model by ReaxFF molecular dynamics simulations

Pei Zhao, Song Han, Xiaoxia Li, Tong Zhu, Xiaofang Tao, Li Guo
Energy & Fuels, 2019, 33 (8), 7176–7187.
DOI: 10.1021/acs.energyfuels.9b01321

Understanding Aldose Reductase-Inhibitors interactions with free energy simulation

Zhaoxi Sun, Xiaohui Wang, Qianqian Zhao, Tong Zhu
Journal of Molecular Graphics and Modelling, 2019, 91, 10–21.
DOI: 10.1016/j.jmgm.2019.05.011

Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations

Jianzhong Chen, Xingyu Wang, Laixue Pang, John ZH Zhang, Tong Zhu
Nucleic acids research, 2019, 47 (13), 6618–6631.
DOI: 10.1093/nar/gkz499

Insights into the binding mechanisms of inhibitors of MDM2 based on molecular dynamics simulations and binding free energy calculations

Pei Zhao, Huali Cao, Yu Chen, Tong Zhu
Chemical Physics Letters, 2019, 728, 94–101.
DOI: 10.1016/j.cplett.2019.05.001

Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations

Jianzhong Chen, Laixue Pang, Wei Wang, Lifei Wang, John ZH Zhang, Tong Zhu
Journal of Biomolecular Structure and Dynamics, 2019.
DOI: 10.1080/07391102.2019.1591304

L-4, a well-tolerated and orally active inhibitor of Hedgehog pathway, exhibited potent anti-tumor effects against medulloblastoma in vitro and in vivo

Mingfei Zhu, Hong Wang, Chenglin Wang, Yanfen Fang, Tong Zhu, Weili Zhao, Xiaochun Dong, Xiongwen Zhang
Frontiers in pharmacology, 2019, 10, 89.
DOI: 10.3389/fphar.2019.00089

A fragment quantum mechanical method for metalloproteins

Mingyuan Xu, Xiao He, Tong Zhu, John ZH Zhang
Journal of chemical theory and computation, 2019, 15 (2), 1430–1439.
DOI: 10.1021/acs.jctc.8b00966

2018

Effect of substituents in different positions of aminothiazole hinge-binding scaffolds on inhibitor--CDK2 association probed by interaction entropy method

Jianzhong Chen, Xingyu Wang, John ZH Zhang, Tong Zhu
ACS Omega, 2018, 3 (12), 18052–18064.
DOI: 10.1021/acsomega.8b02354

Comparison of the unfolding and oligomerization of human prion protein under acidic and neutral environments by molecular dynamics simulations

Ya Gao, Tong Zhu, Chaomin Zhang, John ZH Zhang, Ye Mei
Chemical Physics Letters, 2018, 706, 594–600.
DOI: 10.1016/j.cplett.2018.07.014

Exploring drug-resistant mechanisms of I84V mutation in HIV-1 protease toward different inhibitors by thermodynamics integration and solvated interaction energy method

Ya Gao, Tong Zhu, Jianzhong Chen
Chemical Physics Letters, 2018, 706, 400–408.
DOI: 10.1016/j.cplett.2018.06.040

Donor engineering for NIR-II molecular fluorophores with enhanced fluorescent performance

Qinglai Yang, Zhubin Hu, Shoujun Zhu, Rui Ma, Huilong Ma, Zhuoran Ma, Hao Wan, Tong Zhu, Zhengyan Jiang, Weiqiang Liu, Liying Jiao, Haitao Sun, Yongye Liang, Hongjie Dai
Journal of the American Chemical Society, 2018, 140 (5), 1715–1724.
DOI: 10.1021/jacs.7b10334

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein

Mingyuan Xu, Tong Zhu, John ZH Zhang
Frontiers in chemistry, 2018, 6, 189.
DOI: 10.3389/fchem.2018.00189

A quantum mechanical computational method for modeling electrostatic and solvation effects of protein

Xianwei Wang, Yang Li, Ya Gao, Zejin Yang, Chenhui Lu, Tong Zhu
Scientific reports, 2018, 8 (1), 1–10.
DOI: 10.1038/s41598-018-23783-8

Automated fragmentation QM/MM calculation of NMR chemical shifts for protein-ligand complexes

Xinsheng Jin, Tong Zhu, John ZH Zhang, Xiao He
Frontiers in chemistry, 2018, 6, 150.
DOI: 10.3389/fchem.2018.00150

2017

Structure-based design and synthesis of imidazo [1, 2-a] pyridine derivatives as novel and potent Nek2 inhibitors with in vitro and in vivo antitumor activities

Jian-Bei Xi, Yan-Fen Fang, Brendan Frett, Meng-Li Zhu, Tong Zhu, Yan-Nan Kong, Feng-Jie Guan, Yun Zhao, Xiong-Wen Zhang, Hong-Yu Li, Ming-Liang Ma, Wenhao Hu
European journal of medicinal chemistry, 2017, 126, 1083–1106.
DOI: 10.1016/j.ejmech.2016.12.026

Optimization of convergence criteria for fragmentation methods

Zhaoxi Sun, Tong Zhu, Xiaohui Wang, Ye Mei, John ZH Zhang
Chemical Physics Letters, 2017, 687, 163–170.
DOI: 10.1016/j.cplett.2017.08.059

Origins of Protons in C--H Bond Insertion Products of Phenols: Proton-Self-Sufficient Function via Water Molecules

Zhoujie Luo, Ya Gao, Tong Zhu, John Zenghui Zhang, Fei Xia
The Journal of Physical Chemistry A, 2017, 121 (34), 6523–6529.
DOI: 10.1021/acs.jpca.7b06411

An electrochemical biosensor with dual signal outputs: toward simultaneous quantification of pH and $\ce{O2}$ in the brain upon ischemia and in a tumor during cancer starvation therapy

Li Liu, Fan Zhao, Wei Liu, Tong Zhu, John ZH Zhang, Chen Chen, Zhihui Dai, Huisheng Peng, Jun-Long Huang, Qin Hu, Wenbo Bu, Yang Tian
Angewandte Chemie International Edition, 2017, 56 (35), 10471–10475.
DOI: 10.1002/anie.201705615

Single biosensor for simultaneous quantification of glucose and pH in a rat brain of diabetic model using both current and potential outputs

Shuai Li, Anwei Zhu, Tong Zhu, John ZH Zhang, Yang Tian
Analytical chemistry, 2017, 89 (12), 6656–6662.
DOI: 10.1021/acs.analchem.7b00881

Discovery of Bisindole as a Novel Scaffold for Protein Tyrosine Phosphatase 1B Inhibitors

Changcheng Jing, Ziyan Li, Kaili Jia, Chen Chen, Xiao Liu, Beibei Wang, Wenhao Hu, Jia Li, Tong Zhu, Suzhen Dong
Archiv der Pharmazie, 2017, 350 (1), e1600173.
DOI: 10.1002/ardp.201600173

A theoretical study of the substituent effect on reactions of amines, carbon dioxide and ethylene oxide catalyzed by binary ionic liquids

Minmin Huang, Zhoujie Luo, Tong Zhu, Jian Chen, John Zenghui Zhang, Fei Xia
RSC advances, 2017, 7 (81), 51521–51527.
DOI: 10.1039/C7RA09485J

A test of AMBER force fields in predicting the secondary structure of $\alpha$-helical and $\beta$-hairpin peptides

Ya Gao, Chaomin Zhang, Xianwei Wang, Tong Zhu
Chemical Physics Letters, 2017, 679, 112–118.
DOI: 10.1016/j.cplett.2017.04.074

Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations

Li L Duan, T Zhu, Yu C Li, Qing G Zhang, John ZH Zhang
Scientific reports, 2017, 7 (1), 1–14.
DOI: 10.1038/srep42223

Direct folding simulation of helical proteins using an effective polarizable bond force field

Lili Duan, Tong Zhu, Changge Ji, Qinggang Zhang, John ZH Zhang
Physical Chemistry Chemical Physics, 2017, 19 (23), 15273–15284.
DOI: 10.1039/C7CP02101A

Discovery of core-structurally novel PTP1B inhibitors with specific selectivity containing oxindole-fused spirotetrahydrofurochroman by one-pot reaction

Suzhen Dong, Yubing Lei, Shikun Jia, Lixin Gao, Jia Li, Tong Zhu, Shunying Liu, Wenhao Hu
Bioorganic & medicinal chemistry letters, 2017, 27 (4), 1105–1108.
DOI: 10.1016/j.bmcl.2016.11.055

2016

Predicted PAR1 inhibitors from multiple computational methods

Ying Wang, Jinfeng Liu, Tong Zhu, Lujia Zhang, Xiao He, John ZH Zhang
Chemical Physics Letters, 2016, 659, 295–303.
DOI: 10.1016/j.cplett.2016.07.059

New peptide deformylase inhibitors design, synthesis and pharmacokinetic assessment

Fengping Lv, Chen Chen, Yang Tang, Jianhai Wei, Tong Zhu, Wenhao Hu
Bioorganic & medicinal chemistry letters, 2016, 26 (15), 3714–3718.
DOI: 10.1016/j.bmcl.2016.05.077

PBSA_E: A PBSA-Based Free Energy Estimator for Protein--Ligand Binding Affinity

Xiao Liu, Jinfeng Liu, Tong Zhu, Lujia Zhang, Xiao He, John ZH Zhang
Journal of chemical information and modeling, 2016, 56 (5), 854–861.
DOI: 10.1021/acs.jcim.6b00001

Antitumor activity of TY-011 against gastric cancer by inhibiting Aurora A, Aurora B and VEGFR2 kinases

Wang Liu, Yu Lu, Xiaoping Chai, Xiao Liu, Tong Zhu, Xihan Wu, Yanfen Fang, Xuan Liu, Xiongwen Zhang
Journal of Experimental & Clinical Cancer Research, 2016, 35 (1), 1–15.
DOI: 10.1186/s13046-016-0464-2

A systematic study on RNA NMR chemical shift calculation based on the automated fragmentation QM/MM approach

Xinsheng Jin, Tong Zhu, John ZH Zhang, Xiao He
RSC advances, 2016, 6 (110), 108590–108602.
DOI: 10.1039/C6RA22518G

Preclinical activity of MBM-5 in gastrointestinal cancer by inhibiting NEK2 kinase activity

Yanfen Fang, Yannan Kong, Jianbei Xi, Mengli Zhu, Tong Zhu, Tongtong Jiang, Brendan Frett, Wenhao Hu, Hong-yu Li, Mingliang Ma, others
Oncotarget, 2016, 7 (48), 79327.
DOI: 10.18632/oncotarget.12687

2015

Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method

Tong Zhu, John ZH Zhang, Xiao He
Advance in Structural Bioinformatics, 2015, 49–70.
DOI: 10.1007/978-94-017-9245-5_5

AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules

Jason Swails, Tong Zhu, Xiao He, David A Case
Journal of biomolecular NMR, 2015, 63 (2), 125–139.
DOI: 10.1007/s10858-015-9970-3

A Comparative Insight into Amprenavir Resistance of Mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 Protease Based on Thermodynamic Integration and MM-PBSA Methods

Jianzhong Chen, Xingyu Wang, Tong Zhu, Qinggang Zhang, John ZH Zhang
Journal of chemical information and modeling, 2015, 55 (9), 1903–1913.
DOI: 10.1021/acs.jcim.5b00173

2010-2014

Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations

Tong Zhu, John ZH Zhang, Xiao He
Physical Chemistry Chemical Physics, 2014, 16 (34), 18163–18169.
DOI: 10.1039/C4CP02553A

Fragment Quantum Mechanical Calculation of Proteins and Its Applications

Xiao He, Tong Zhu, Xianwei Wang, Jinfeng Liu, John ZH Zhang
Accounts of chemical research, 2014, 47 (9), 2748–2757.
DOI: 10.1021/ar500077t

Electronic polarization stabilizes tertiary structure prediction of HP-36

Li L Duan, Tong Zhu, Qing G Zhang, Bo Tang, John ZH Zhang
Journal of molecular modeling, 2014, 20 (4), 1–19.
DOI: 10.1007/s00894-014-2195-7

Asp120Asn mutation impairs the catalytic activity of NDM-1 metallo-$\beta$-lactamase: experimental and computational study

Jiao Chen, Hui Chen, Tong Zhu, Dandan Zhou, Fang Zhang, Xingzhen Lao, Heng Zheng
Physical Chemistry Chemical Physics, 2014, 16 (14), 6709–6716.
DOI: 10.1039/C3CP55069A

Automated fragmentation QM/MM calculation of amide proton chemical shifts in proteins with explicit solvent model

Tong Zhu, John ZH Zhang, Xiao He
Journal of chemical theory and computation, 2013, 9 (4), 2104–2114.
DOI: 10.1021/ct300999w

A New Quantum Calibrated Force Field for Zinc–Protein Complex

Tong Zhu, Xudong Xiao, Changge Ji, John ZH Zhang
Journal of chemical theory and computation, 2013, 9 (3), 1788–1798.
DOI: 10.1021/ct301091z

An implementation of hydrophobic force in implicit solvent molecular dynamics simulation for packed proteins

Li L Duan, Tong Zhu, Ye Mei, Qing G Zhang, Bo Tang, John ZH Zhang
Journal of molecular modeling, 2013, 19 (6), 2605–2612.
DOI: 10.1007/s00894-013-1798-8

Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation

Tong Zhu, Xiao He, John ZH Zhang
Physical Chemistry Chemical Physics, 2012, 14 (21), 7837–7845.
DOI: 10.1039/C2CP23746F

Quasi-classical Trajectory Study of Reaction $\ce{O (^3P) + HCl (v= 2; j= 1, 6, 9) -> OH + Cl}$

Tong Zhu, Guo-Dong Hu, Qing-Gang Zhang
Chinese Physics Letters, 2010, 27 (3), 033102.
DOI: 10.1088/0256-307X/27/3/033102

Theoretical study of stereodynamics for reaction $\ce{O (^3P) + HCl}$

Tong Zhu, Guo-Dong Hu, Jian-Zhong Chen, Xin-Guo Liu, Qing-Gang Zhang
Chinese Physics B, 2010, 19 (8), 083402.
DOI: 10.1088/1674-1056/19/8/083402

Quasi-classical trajectory study of the reaction $\ce{O (^3P) + HCl -> OH + Cl}$ and $\ce{O (^3P) + DCl -> OD + Cl}$: Vector and scalar properties

Tong Zhu, Guodong Hu, Qinggang Zhang
Journal of Molecular Structure: THEOCHEM, 2010, 948 (1-3), 36–42.
DOI: 10.1016/j.theochem.2010.02.015

THE EFFECT OF VIBRATIONAL EXCITATION OF THE REACTION $\ce{O (^3 P) + HCl -> OH + Cl}$ FOR THE $^3 A^{″}$ ELECTRONIC STATES

Huirong Liu, Xinguo Liu, Tong Zhu, Haizhu Sun, Qinggang Zhang
Journal of Theoretical and Computational Chemistry, 2010, 9 (06), 1033–1042.
DOI: 10.1142/S0219633610006183

Some insights into mechanism for binding and drug resistance of wild type and I50V V82A and I84V mutations in HIV-1 protease with GRL-98065 inhibitor from molecular dynamic simulations

Guo-Dong Hu, Tong Zhu, Shao-Long Zhang, Dunyou Wang, Qing-Gang Zhang
European journal of medicinal chemistry, 2010, 45 (1), 227–235.
DOI: 10.1016/j.ejmech.2009.09.048

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\ No newline at end of file diff --git a/reacnetgenerator/index.html b/reacnetgenerator/index.html index 6a4c6026e..75e74027b 100644 --- a/reacnetgenerator/index.html +++ b/reacnetgenerator/index.html @@ -1 +1 @@ -ReacNetGenerator | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

ReacNetGenerator

An automatic generator of reaction network for reactive molecular dynamics simulation

Citation and contact

ReacNetGenerator: an Automatic Reaction Network Generator for Reactive Molecular Dynamic Simulations, Phys. Chem. Chem. Phys., 2019, doi: 10.1039/C9CP05091D

jinzhe.zeng@rutgers.edu (Jinzhe Zeng), tzhu@lps.ecnu.edu.cn (Tong Zhu)

Installation

First, you need to download the source code from the Releases page.

Then install ReacNetGenerator with one of the following guides:

Building a conda package

1. Install Anaconda or Miniconda to obtain conda.

2. Decompress reacnetgenerator.zip and build in the main directory of ReacNetGenerator:

1
2
3
4
conda config --add channels conda-forge
conda build conda/recipe
conda install reacnetgenerator --use-local
reacnetgenerator -h

Building a Docker Image

1.Install Docker.

2.Decompress reacnetgenerator.zip and build in the main directory of ReacNetGenerator:

1
2
docker build . -t njzjz/reacnetgenerator
docker run njzjz/reacnetgenerator reacnetgenerator -h

Usage

Command line

ReacNetGenerator can process any kind of trajectory files containing atomic coordinates, e.g. a LAMMPS dump file prepared by running “dump 1 all custom 100 dump.reaxc id type x y z” in LAMMPS:

1
reacnetgenerator --dump -i dump.reaxc -a C H O

where C, H, and O are atomic names in the input file. Analysis report will be generated automatically.

Also, ReacNetGenerator can process files containing bond information, e.g. LAMMPS bond file:

1
reacnetgenerator -i bonds.reaxc -a C H O

You can run the following script for help:

1
reacnetgenerator -h

GUI version

You can open a GUI version for ReacNetGenerator by typing:

1
reacnetgeneratorgui

Awards

  • The First Prize in 2019 (the 11th Session) Shanghai Computer Application Competition for College Students (2019年（第十一届）上海市大学生计算机应用能力大赛一等奖)
  • The First Prize in 2019 (the 12th Session) Chinese Computer Design Competition for College Students (2019年（第12届）中国大学生计算机设计大赛一等奖)

Acknowledge

  • National Natural Science Foundation of China (Grants No. 91641116)
  • National Innovation and Entrepreneurship Training Program for Undergraduate (201910269080)
  • ECNU Multifunctional Platform for Innovation (No. 001)
0%
\ No newline at end of file +ReacNetGenerator | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

ReacNetGenerator

An automatic generator of reaction network for reactive molecular dynamics simulation

Citation and contact

ReacNetGenerator: an Automatic Reaction Network Generator for Reactive Molecular Dynamic Simulations, Phys. Chem. Chem. Phys., 2019, doi: 10.1039/C9CP05091D

jinzhe.zeng@rutgers.edu (Jinzhe Zeng), tzhu@lps.ecnu.edu.cn (Tong Zhu)

Installation

First, you need to download the source code from the Releases page.

Then install ReacNetGenerator with one of the following guides:

Building a conda package

1. Install Anaconda or Miniconda to obtain conda.

2. Decompress reacnetgenerator.zip and build in the main directory of ReacNetGenerator:

1
2
3
4
conda config --add channels conda-forge
conda build conda/recipe
conda install reacnetgenerator --use-local
reacnetgenerator -h

Building a Docker Image

1.Install Docker.

2.Decompress reacnetgenerator.zip and build in the main directory of ReacNetGenerator:

1
2
docker build . -t njzjz/reacnetgenerator
docker run njzjz/reacnetgenerator reacnetgenerator -h

Usage

Command line

ReacNetGenerator can process any kind of trajectory files containing atomic coordinates, e.g. a LAMMPS dump file prepared by running “dump 1 all custom 100 dump.reaxc id type x y z” in LAMMPS:

1
reacnetgenerator --dump -i dump.reaxc -a C H O

where C, H, and O are atomic names in the input file. Analysis report will be generated automatically.

Also, ReacNetGenerator can process files containing bond information, e.g. LAMMPS bond file:

1
reacnetgenerator -i bonds.reaxc -a C H O

You can run the following script for help:

1
reacnetgenerator -h

GUI version

You can open a GUI version for ReacNetGenerator by typing:

1
reacnetgeneratorgui

Awards

  • The First Prize in 2019 (the 11th Session) Shanghai Computer Application Competition for College Students (2019年（第十一届）上海市大学生计算机应用能力大赛一等奖)
  • The First Prize in 2019 (the 12th Session) Chinese Computer Design Competition for College Students (2019年（第12届）中国大学生计算机设计大赛一等奖)

Acknowledge

  • National Natural Science Foundation of China (Grants No. 91641116)
  • National Innovation and Entrepreneurship Training Program for Undergraduate (201910269080)
  • ECNU Multifunctional Platform for Innovation (No. 001)
0%
\ No newline at end of file diff --git a/research/index.html b/research/index.html index 9e6d4c48f..18681cfb2 100644 --- a/research/index.html +++ b/research/index.html @@ -1 +1 @@ -Research | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Research

The research interest in this Lab is mainly focused on three topics:

  • Multiscale simulation of interactions between metal ions and protein/nucleic acid

  • Reaction mechanism of complex chemical systems.

 

  • Computer-aided drug design.

Funding Support

  • NSF Key Program (2017-2019)
  • NYU-ECNU seed grant (2017-2018)
  • National Key R&D Program of China (2017-2021)
  • NSF General Program for Young Scholars (2015-2017)
  • China Postdoctoral Research Project
0%
\ No newline at end of file +Research | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Research

The research interest in this Lab is mainly focused on three topics:

  • Multiscale simulation of interactions between metal ions and protein/nucleic acid

  • Reaction mechanism of complex chemical systems.

 

  • Computer-aided drug design.

Funding Support

  • NSF Key Program (2017-2019)
  • NYU-ECNU seed grant (2017-2018)
  • National Key R&D Program of China (2017-2021)
  • NSF General Program for Young Scholars (2015-2017)
  • China Postdoctoral Research Project
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\ No newline at end of file diff --git a/sitemap.xml b/sitemap.xml index 99cde4372..41bccc3e9 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -202,7 +202,7 @@ https://computchem.cn/ - 2023-07-12 + 2023-07-26 daily 1.0 @@ -212,14 +212,14 @@ https://computchem.cn/categories/News/ - 2023-07-12 + 2023-07-26 weekly 0.2 https://computchem.cn/categories/uncategorized/ - 2023-07-12 + 2023-07-26 weekly 0.2 diff --git a/softwares/index.html b/softwares/index.html index 85f3f517e..2d355404e 100644 --- a/softwares/index.html +++ b/softwares/index.html @@ -1 +1 @@ -Softwares | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Softwares

SHIFTS

ReacNetGenerator

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\ No newline at end of file +Softwares | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Softwares

SHIFTS

ReacNetGenerator

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Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Teaching

2019 Fall Semester, Application of Quantum Chemistry and Molecular modeling in Chemistry, for graduate students @ECNU

2019 Spring Semester, Structural Chemistry, for undergraduate students @ECNU

2018 Spring Semester, Structural Chemistry, for undergraduate students @ECNU

2018 Spring Semester, Computational Chemistry, for undergraduate students @ECNU

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\ No newline at end of file +Teaching | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Teaching

2019 Fall Semester, Application of Quantum Chemistry and Molecular modeling in Chemistry, for graduate students @ECNU

2019 Spring Semester, Structural Chemistry, for undergraduate students @ECNU

2018 Spring Semester, Structural Chemistry, for undergraduate students @ECNU

2018 Spring Semester, Computational Chemistry, for undergraduate students @ECNU

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\ No newline at end of file diff --git a/tips/index.html b/tips/index.html index 5553d2d53..53bffaaff 100644 --- a/tips/index.html +++ b/tips/index.html @@ -1 +1 @@ -Tips | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Tips

  1. [转载] DeepMD-kit v1.0 和 TensorFlow的安装 (曾晋哲)
  2. CP2K 6.1 安装 (intel 编译器) CP2K install with intel complier. (曹立群)
  3. CentOS 7 Pymol 编译 (Install pymol from source code) (朱通)
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\ No newline at end of file +Tips | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

Tips

  1. [转载] DeepMD-kit v1.0 和 TensorFlow的安装 (曾晋哲)
  2. CP2K 6.1 安装 (intel 编译器) CP2K install with intel complier. (曹立群)
  3. CentOS 7 Pymol 编译 (Install pymol from source code) (朱通)
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\ No newline at end of file diff --git "a/\350\275\254\350\275\275-\345\256\211\350\243\205-deepmd-kit-v1-0/index.html" "b/\350\275\254\350\275\275-\345\256\211\350\243\205-deepmd-kit-v1-0/index.html" index f5e8449f3..86fdf849e 100644 --- "a/\350\275\254\350\275\275-\345\256\211\350\243\205-deepmd-kit-v1-0/index.html" +++ "b/\350\275\254\350\275\275-\345\256\211\350\243\205-deepmd-kit-v1-0/index.html" @@ -1 +1 @@ -[转载] 安装 DeepMD-kit v1.0 | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

[转载] 安装 DeepMD-kit v1.0

原作者：曾晋哲

原链接： https://mp.weixin.qq.com/s/DeQZKwoyxXK7rHhhmdgTmw https://mp.weixin.qq.com/s/MsEtgnN\_mi-auiFyXYUquA

假定已经安装了Anaconda（建议使用最新版2019.07），已连接互联网，则

1.安装tensorflow（如仅需CPU版本的TensorFlow，则将tensorflow-gpu改为tensorflow）：

1
python -m pip install tensorflow Successfully installed google-pasta-0.1.7 keras-applications-1.0.8 opt-einsum-3.1.0 tensorboard-2.0.0 tensorflow-estimator-2.0.0 tensorflow-gpu-2.0.0

2.安装deepmd-kit v1.0：

1
python -m pip install git+https://github.com/deepmodeling/deepmd-kit

Building wheels for collected packages: deepmd-kit
Building wheel for deepmd-kit (PEP 517) … done
Created wheel for deepmd-kit: filename=deepmd_kit-1.0.0-cp37-cp37m-linux_x86_64.whl size=268836 sha256=1f5b1149bbf35c0c96c713cc8b607e0626ad0df6451a7 171d4f6b46acc2d4290
Stored in directory: /tmp/pip-ephem-wheel-cache-zlksq4dl/wheels/a2/80/6c/a26fba79e43199eb4cdba7a3686c5370d3620916f5a0ea23ac
Successfully built deepmd-kit
Installing collected packages: deepmd-kit
Successfully built deepmd-kit
Installing collected packages: deepmd-kit
Successfully installed deepmd-kit-1.0.0

大功告成！现在看一看是否成功安装：

1
dp -h

usage: dp [-h] {train,freeze,test} …
DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics
optional arguments:  -h, –help
          show this help message and exit Valid subcommands:  {train,freeze,test}
   train              train a model
   freeze             freeze the model
   test               test the model

现在，DeePMD-kit v1.0.0已成功安装。下一期将介绍如何用DP编译LAMMPS

TensorFlow 安装

最新版本的 TensorFlow 要求 GLIBC 2.17 以上，尽管推荐做法是找一台最新系统的机子，但是有时候系统的类型不是由自己决定的，通常又没有root权限，又想在所有机子上都能运行 TensorFlow 。 刚好手里有一个超算账号，系统是 Red Hat 4.4.7 ，GLIBC 版本是 2.12 ，就以此为例，安装CPU版本的TensorFlow（反正没有权限也安装不了GPU版本需要的驱动）。

一、用 Anaconda 3 安装 TensorFlow 1.8

1.安装 Anaconda 3 见Linux软件安装②Anaconda3 2.创建 TensorFlow 环境

1
2
3
4
5
conda create -n tensorflow pip python=3.6
#Proceed ([y]/n)? 输y
source activate tensorflow #激活环境
pip install tensorflow -i https://pypi.tuna.tsinghua.edu.cn/simple/
#这两天由于众所周知的原因，Google官方的镜像又下载不了了，所以这里用了清华大学的镜像

二、安装 gcc

这时候打开 Python ，执行 import tensorflow ，提示：

ImportError: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.7’ not found

1
2
3
conda install -c psi4 gcc-5 
#Proceed ([y]/n)? 输y
LD_LIBRARY_PATH=$HOME/anaconda3/envs/tensorflow/lib:$LD_LIBRARY_PATH

再此运行 Python，不再提示这个问题。

三、安装 GLIBC 2.21

但是提示：

ImportError: /lib64/libc.so.6: version `GLIBC_2.16’ not found

本来应该安装GLIBC 2.17，但是我发现从2.16到2.19都有个bug，不能运行Python 3.6。于是我们安装GLIBC 2.21。 1.下载GLIBC 2.21并编译GLIBC 2.21

1
2
3
4
5
6
wget http://mirror.rit.edu/gnu/libc/glibc-2.21.tar.gz
tar zxvf glibc-2.21.tar.gz
mkdir glibc-2.21-build glibc-2.21-install
cd glibc-2.21-build
../glibc-2.21/configure --prefix=`readlink -f ../glibc-2.21-install` 
make && make install

然后就报错了：

checking version of as… 2.20.51.0.2, bad checking version of ld… 2.20.51.0.2, bad These critical programs are missing or too old: as ld

仔细看看INSTALL文件，要求GNU ‘binutils’ 2.22 or later，但系统只装了2.20。 2.下载并编译binutils 2.30

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3
4
5
6
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wget ftp://ftp.gnu.org/gnu/binutils/binutils-2.30.tar.gz
tar zxvf binutils-2.30.tar.gz
cd binutils-2.30
./configure --prefix=`readlink -f ../binutils-2.30-install` 
make && make install
#加入环境变量
PATH=$HOME/software/binutils-2.30-install/bin:$PATH

3.重新编译glibc 2.21

1
2
3
cd glibc-2.21-build
../glibc-2.21/configure --prefix=`readlink -f ../glibc-2.21-install` 
make && make install

Warning: ignoring configuration file that cannot be opened: … /software/glibc-2.21-install/etc/ld.so.conf: No such file or directory

将/etc 目录的ld.so.conf复制到指定目录后重新安装：

1
2
cp /etc/ld.so.conf ../glibc-2.21-install/etc/
make install

安装成功。

四、运行TensorFlow

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source activate tensorflow
$HOME/software/glibc-2.21-install/lib/ld-2.21.so --library-path $HOME/anaconda3/envs/tensorflow/lib:$HOME/software/glibc-2.21-install/lib:/lib64:$LD_LIBRARY_PATH `which python`

在Python内输入：

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# Python
import tensorflow as tf
hello = tf.constant('Hello, TensorFlow!')
sess = tf.Session()
print(sess.run(hello))

b’Hello, TensorFlow!’

运行成功。我们可以运行的命令记录在.bashrc中：

1
echo 'alias tf='"'"'$HOME/software/glibc-2.21-install/lib/ld-2.21.so --library-path $HOME/anaconda3/envs/tensorflow/lib:$HOME/software/glib-2.21-install/lib:/lib64:$LD_LIBRARY_PATH `which python`'"'">>$HOME/.bashrcsource $HOME/.bashrc

即可用 tf 代替装了 TensorFlow 的 Python。

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\ No newline at end of file +[转载] 安装 DeepMD-kit v1.0 | Tong Zhu Research Group

Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

[转载] 安装 DeepMD-kit v1.0

原作者：曾晋哲

原链接： https://mp.weixin.qq.com/s/DeQZKwoyxXK7rHhhmdgTmw https://mp.weixin.qq.com/s/MsEtgnN\_mi-auiFyXYUquA

假定已经安装了Anaconda（建议使用最新版2019.07），已连接互联网，则

1.安装tensorflow（如仅需CPU版本的TensorFlow，则将tensorflow-gpu改为tensorflow）：

1
python -m pip install tensorflow Successfully installed google-pasta-0.1.7 keras-applications-1.0.8 opt-einsum-3.1.0 tensorboard-2.0.0 tensorflow-estimator-2.0.0 tensorflow-gpu-2.0.0

2.安装deepmd-kit v1.0：

1
python -m pip install git+https://github.com/deepmodeling/deepmd-kit

Building wheels for collected packages: deepmd-kit
Building wheel for deepmd-kit (PEP 517) … done
Created wheel for deepmd-kit: filename=deepmd_kit-1.0.0-cp37-cp37m-linux_x86_64.whl size=268836 sha256=1f5b1149bbf35c0c96c713cc8b607e0626ad0df6451a7 171d4f6b46acc2d4290
Stored in directory: /tmp/pip-ephem-wheel-cache-zlksq4dl/wheels/a2/80/6c/a26fba79e43199eb4cdba7a3686c5370d3620916f5a0ea23ac
Successfully built deepmd-kit
Installing collected packages: deepmd-kit
Successfully built deepmd-kit
Installing collected packages: deepmd-kit
Successfully installed deepmd-kit-1.0.0

大功告成！现在看一看是否成功安装：

1
dp -h

usage: dp [-h] {train,freeze,test} …
DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics
optional arguments:  -h, –help
          show this help message and exit Valid subcommands:  {train,freeze,test}
   train              train a model
   freeze             freeze the model
   test               test the model

现在，DeePMD-kit v1.0.0已成功安装。下一期将介绍如何用DP编译LAMMPS

TensorFlow 安装

最新版本的 TensorFlow 要求 GLIBC 2.17 以上，尽管推荐做法是找一台最新系统的机子，但是有时候系统的类型不是由自己决定的，通常又没有root权限，又想在所有机子上都能运行 TensorFlow 。 刚好手里有一个超算账号，系统是 Red Hat 4.4.7 ，GLIBC 版本是 2.12 ，就以此为例，安装CPU版本的TensorFlow（反正没有权限也安装不了GPU版本需要的驱动）。

一、用 Anaconda 3 安装 TensorFlow 1.8

1.安装 Anaconda 3 见Linux软件安装②Anaconda3 2.创建 TensorFlow 环境

1
2
3
4
5
conda create -n tensorflow pip python=3.6
#Proceed ([y]/n)? 输y
source activate tensorflow #激活环境
pip install tensorflow -i https://pypi.tuna.tsinghua.edu.cn/simple/
#这两天由于众所周知的原因，Google官方的镜像又下载不了了，所以这里用了清华大学的镜像

二、安装 gcc

这时候打开 Python ，执行 import tensorflow ，提示：

ImportError: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.7’ not found

1
2
3
conda install -c psi4 gcc-5 
#Proceed ([y]/n)? 输y
LD_LIBRARY_PATH=$HOME/anaconda3/envs/tensorflow/lib:$LD_LIBRARY_PATH

再此运行 Python，不再提示这个问题。

三、安装 GLIBC 2.21

但是提示：

ImportError: /lib64/libc.so.6: version `GLIBC_2.16’ not found

本来应该安装GLIBC 2.17，但是我发现从2.16到2.19都有个bug，不能运行Python 3.6。于是我们安装GLIBC 2.21。 1.下载GLIBC 2.21并编译GLIBC 2.21

1
2
3
4
5
6
wget http://mirror.rit.edu/gnu/libc/glibc-2.21.tar.gz
tar zxvf glibc-2.21.tar.gz
mkdir glibc-2.21-build glibc-2.21-install
cd glibc-2.21-build
../glibc-2.21/configure --prefix=`readlink -f ../glibc-2.21-install` 
make && make install

然后就报错了：

checking version of as… 2.20.51.0.2, bad checking version of ld… 2.20.51.0.2, bad These critical programs are missing or too old: as ld

仔细看看INSTALL文件，要求GNU ‘binutils’ 2.22 or later，但系统只装了2.20。 2.下载并编译binutils 2.30

1
2
3
4
5
6
7
wget ftp://ftp.gnu.org/gnu/binutils/binutils-2.30.tar.gz
tar zxvf binutils-2.30.tar.gz
cd binutils-2.30
./configure --prefix=`readlink -f ../binutils-2.30-install` 
make && make install
#加入环境变量
PATH=$HOME/software/binutils-2.30-install/bin:$PATH

3.重新编译glibc 2.21

1
2
3
cd glibc-2.21-build
../glibc-2.21/configure --prefix=`readlink -f ../glibc-2.21-install` 
make && make install

Warning: ignoring configuration file that cannot be opened: … /software/glibc-2.21-install/etc/ld.so.conf: No such file or directory

将/etc 目录的ld.so.conf复制到指定目录后重新安装：

1
2
cp /etc/ld.so.conf ../glibc-2.21-install/etc/
make install

安装成功。

四、运行TensorFlow

1
2
source activate tensorflow
$HOME/software/glibc-2.21-install/lib/ld-2.21.so --library-path $HOME/anaconda3/envs/tensorflow/lib:$HOME/software/glibc-2.21-install/lib:/lib64:$LD_LIBRARY_PATH `which python`

在Python内输入：

1
2
3
4
5
# Python
import tensorflow as tf
hello = tf.constant('Hello, TensorFlow!')
sess = tf.Session()
print(sess.run(hello))

b’Hello, TensorFlow!’

运行成功。我们可以运行的命令记录在.bashrc中：

1
echo 'alias tf='"'"'$HOME/software/glibc-2.21-install/lib/ld-2.21.so --library-path $HOME/anaconda3/envs/tensorflow/lib:$HOME/software/glib-2.21-install/lib:/lib64:$LD_LIBRARY_PATH `which python`'"'">>$HOME/.bashrcsource $HOME/.bashrc

即可用 tf 代替装了 TensorFlow 的 Python。

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\ No newline at end of file