Complete the DRH -> NA change

lorenzo-rovigatti · Nov 15, 2023 · aaebaeb · aaebaeb
1 parent 8f2fc5f
commit aaebaeb
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Showing 4 changed files with 21 additions and 4 deletions.
diff --git a/CHANGELOG b/CHANGELOG
@@ -1,4 +1,21 @@
-v. 3.5.2
+v. 3.6.0
+	- Add 6 more tests to the `run` level; these tests use the new topology and check that the DNA, RNA and NA interactions compute the right energies for a short nicked duplex
+	- Add support for a "new" topology format where nucleotides are listed in the 5' -> 3' order, which is the standard in the community
+	- Add the NA interaction, which can be used to simulate hybrid DNA/RNA systems (by @eryykr, see #68)
+	- Add a old<->new topology converter to the `utils` folder
+	- Add an option `stiff_rate` to the `mutual_trap` force
+	- Remove a few warnings when compiling with CUDA
+	- Fix the computation of the stress tensor on the GPU
+	oxpy:
+	  - Update pybind to make oxpy compatible with newer Python versions
+	  - Deprecate support for Python versions < 3.8
+	  - Add (undocumented) support for `-Dpython=On` and `-DPYTHON=On`
+	oat:
+	  - Add support for the new topology format
+	  - Fixed an error in the oxDNA_PDB CLI parser
+	  - Added error handling for truncated trajectories in the oat parser (see #67)
+
+v. 3.5.2 [50479f2]
 	oat: 
 	  - remove usage of `|` to specify type annotations for unions to make oat compatible with Python 3.9
       - improve the portability of the `setup.py` script to fix installation issues on some systems

diff --git a/DRH_sequence_dependent_parameters.txt → NA_sequence_dependent_parameters.txt b/DRH_sequence_dependent_parameters.txt → NA_sequence_dependent_parameters.txt
diff --git a/test/DNA_RNA/FORCE_FIELD/AVG_SEQ/run_input b/test/DNA_RNA/FORCE_FIELD/AVG_SEQ/run_input
@@ -14,7 +14,7 @@ T = 20C
 dt = 0.005
 verlet_skin = 0.05
 
-interaction_type = DRH
+interaction_type = NA
 salt_concentration = 1.0
 
 ####    INPUT / OUTPUT    ####

diff --git a/test/DNA_RNA/FORCE_FIELD/SEQ_DEP/run_input b/test/DNA_RNA/FORCE_FIELD/SEQ_DEP/run_input
@@ -14,10 +14,10 @@ T = 20C
 dt = 0.005
 verlet_skin = 0.05
 
-interaction_type = DRH
+interaction_type = NA
 salt_concentration = 1.0
 use_average_seq = true
-seq_dep_file = ../../../../DRH_sequence_dependent_parameters.txt
+seq_dep_file = ../../../../NA_sequence_dependent_parameters.txt
 
 ####    INPUT / OUTPUT    ####
 topology = ../init.top