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corrected the impropers in oplsaa.lt. (I commented out the "allenes i…
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…mproper" interactions because they were causing trouble. The were not in the original 2008 version of OPLSAA, so they are a lower priority. I will revisit them later.)
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@jewettaij
jewettaij committed Dec 3, 2024
1 parent 84505d7 commit 1c57100
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28 changes: 14 additions & 14 deletions examples/all_atom/force_field_OPLSAA/benzene+benzoic_acid/moltemplate_files/benzene.lt
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Expand Up @@ -3,8 +3,8 @@ import "oplsaa.lt"
# The "oplsaa.lt" file contains force-field parameters, atom type definitions,
# partial charges, masses and bond-angle rules for the atoms in your system.
# Note:
# Atom type @atom:145 corresponds to "Benzene C"
# Atom type @atom:146 corresponds to "Benzene H"
# Atom type @atom:145 corresponds to "C - CA | Benzene C"
# Atom type @atom:146 corresponds to "H - HA | Benzene H"



Expand All @@ -13,18 +13,18 @@ Benzene inherits OPLSAA {
# atom-id mol-id atom-type charge X Y Z # comment

write("Data Atoms") {
$atom:c1 $mol @atom:145 0.00 -0.739 1.189 -0.00733 # @atom:145 <--> Benzene C
$atom:c2 $mol @atom:145 0.00 0.614 1.208 0.35167 # @atom:145 <--> Benzene C
$atom:c3 $mol @atom:145 0.00 1.353 0.019 0.35867 # @atom:145 <--> Benzene C
$atom:c4 $mol @atom:145 0.00 0.739 -1.189 0.00667 # @atom:145 <--> Benzene C
$atom:c5 $mol @atom:145 0.00 -0.614 -1.208 -0.35133 # @atom:145 <--> Benzene C
$atom:c6 $mol @atom:145 0.00 -1.353 -0.019 -0.35833 # @atom:145 <--> Benzene C
$atom:h1 $mol @atom:146 0.00 -1.309 2.106 -0.01233 # @atom:146 <--> Benzene H
$atom:h2 $mol @atom:146 0.00 1.088 2.14 0.62267 # @atom:146 <--> Benzene H
$atom:h3 $mol @atom:146 0.00 2.397 0.034 0.63467 # @atom:146 <--> Benzene H
$atom:h4 $mol @atom:146 0.00 1.309 -2.106 0.01267 # @atom:146 <--> Benzene H
$atom:h5 $mol @atom:146 0.00 -1.088 -2.14 -0.62233 # @atom:146 <--> Benzene H
$atom:h6 $mol @atom:146 0.00 -2.397 -0.034 -0.63533 # @atom:146 <--> Benzene H
$atom:c1 $mol @atom:145 0.00 -0.739 1.189 -0.00733 # @atom:145 --> C - CA | Benzene C
$atom:c2 $mol @atom:145 0.00 0.614 1.208 0.35167 # @atom:145 --> C - CA | Benzene C
$atom:c3 $mol @atom:145 0.00 1.353 0.019 0.35867 # @atom:145 --> C - CA | Benzene C
$atom:c4 $mol @atom:145 0.00 0.739 -1.189 0.00667 # @atom:145 --> C - CA | Benzene C
$atom:c5 $mol @atom:145 0.00 -0.614 -1.208 -0.35133 # @atom:145 --> C - CA | Benzene C
$atom:c6 $mol @atom:145 0.00 -1.353 -0.019 -0.35833 # @atom:145 --> C - CA | Benzene C
$atom:h1 $mol @atom:146 0.00 -1.309 2.106 -0.01233 # @atom:146 --> H - HA | Benzene H
$atom:h2 $mol @atom:146 0.00 1.088 2.14 0.62267 # @atom:146 --> H - HA | Benzene H
$atom:h3 $mol @atom:146 0.00 2.397 0.034 0.63467 # @atom:146 --> H - HA | Benzene H
$atom:h4 $mol @atom:146 0.00 1.309 -2.106 0.01267 # @atom:146 --> H - HA | Benzene H
$atom:h5 $mol @atom:146 0.00 -1.088 -2.14 -0.62233 # @atom:146 --> H - HA | Benzene H
$atom:h6 $mol @atom:146 0.00 -2.397 -0.034 -0.63533 # @atom:146 --> H - HA | Benzene H
}

# Note: You don't have to specify the charge in this example because we are
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10,381 changes: 0 additions & 10,381 deletions examples/all_atom/force_field_OPLSAA/benzene+benzoic_acid/moltemplate_files/oplsaa.lt
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10,381 changes: 0 additions & 10,381 deletions examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/oplsaa.lt
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28 changes: 14 additions & 14 deletions examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/benzene.lt
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@ import "oplsaa.lt"
# The "oplsaa.lt" file contains force-field parameters, atom type definitions,
# partial charges, masses and bond-angle rules for the atoms in your system.
# Note:
# Atom type @atom:145 corresponds to "Benzene C"
# Atom type @atom:146 corresponds to "Benzene H"
# Atom type @atom:145 corresponds to "C - CA | Benzene C"
# Atom type @atom:146 corresponds to "H - HA | Benzene H"



Expand All @@ -13,18 +13,18 @@ Benzene inherits OPLSAA {
# atom-id mol-id atom-type charge X Y Z # comment

write("Data Atoms") {
$atom:c1 $mol @atom:145 0.00 -0.739 1.189 -0.00733 # @atom:145 <--> Benzene C
$atom:c2 $mol @atom:145 0.00 0.614 1.208 0.35167 # @atom:145 <--> Benzene C
$atom:c3 $mol @atom:145 0.00 1.353 0.019 0.35867 # @atom:145 <--> Benzene C
$atom:c4 $mol @atom:145 0.00 0.739 -1.189 0.00667 # @atom:145 <--> Benzene C
$atom:c5 $mol @atom:145 0.00 -0.614 -1.208 -0.35133 # @atom:145 <--> Benzene C
$atom:c6 $mol @atom:145 0.00 -1.353 -0.019 -0.35833 # @atom:145 <--> Benzene C
$atom:h1 $mol @atom:146 0.00 -1.309 2.106 -0.01233 # @atom:146 <--> Benzene H
$atom:h2 $mol @atom:146 0.00 1.088 2.14 0.62267 # @atom:146 <--> Benzene H
$atom:h3 $mol @atom:146 0.00 2.397 0.034 0.63467 # @atom:146 <--> Benzene H
$atom:h4 $mol @atom:146 0.00 1.309 -2.106 0.01267 # @atom:146 <--> Benzene H
$atom:h5 $mol @atom:146 0.00 -1.088 -2.14 -0.62233 # @atom:146 <--> Benzene H
$atom:h6 $mol @atom:146 0.00 -2.397 -0.034 -0.63533 # @atom:146 <--> Benzene H
$atom:c1 $mol @atom:145 0.00 -0.739 1.189 -0.00733 # @atom:145 --> C - CA | Benzene C
$atom:c2 $mol @atom:145 0.00 0.614 1.208 0.35167 # @atom:145 --> C - CA | Benzene C
$atom:c3 $mol @atom:145 0.00 1.353 0.019 0.35867 # @atom:145 --> C - CA | Benzene C
$atom:c4 $mol @atom:145 0.00 0.739 -1.189 0.00667 # @atom:145 --> C - CA | Benzene C
$atom:c5 $mol @atom:145 0.00 -0.614 -1.208 -0.35133 # @atom:145 --> C - CA | Benzene C
$atom:c6 $mol @atom:145 0.00 -1.353 -0.019 -0.35833 # @atom:145 --> C - CA | Benzene C
$atom:h1 $mol @atom:146 0.00 -1.309 2.106 -0.01233 # @atom:146 --> H - HA | Benzene H
$atom:h2 $mol @atom:146 0.00 1.088 2.14 0.62267 # @atom:146 --> H - HA | Benzene H
$atom:h3 $mol @atom:146 0.00 2.397 0.034 0.63467 # @atom:146 --> H - HA | Benzene H
$atom:h4 $mol @atom:146 0.00 1.309 -2.106 0.01267 # @atom:146 --> H - HA | Benzene H
$atom:h5 $mol @atom:146 0.00 -1.088 -2.14 -0.62233 # @atom:146 --> H - HA | Benzene H
$atom:h6 $mol @atom:146 0.00 -2.397 -0.034 -0.63533 # @atom:146 --> H - HA | Benzene H
}

# Note: You don't have to specify the charge in this example because we are
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16 changes: 8 additions & 8 deletions examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/ethylene.lt
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@ import "oplsaa.lt"
# The "oplsaa.lt" file contains force-field parameters, atom type definitions,
# partial charges, masses and bond-angle rules for the atoms in your system.
# Note:
# Atom type 143 corresponds to "alkene C (H2-C=)"
# Atom type 144 corresponds to "alkene H (H-C=)"
# Atom type 143 corresponds to "C - CM | alkene C (H2-C=)"
# Atom type 144 corresponds to "H - HC | alkene H (H-C=)"



Expand All @@ -13,12 +13,12 @@ Ethylene inherits OPLSAA {
# atom-id mol-id atom-type charge X Y Z # comment

write('Data Atoms') {
$atom:c1 $mol @atom:143 0.0 -0.6695 0.00000 0.0 #143->"alkene C (H2-C=)"
$atom:c2 $mol @atom:143 0.0 0.6695 0.00000 0.0 #143->"alkene C (H2-C=)"
$atom:h11 $mol @atom:144 0.0 -1.23422 -0.85446 0.0 #144->"alkene H (H-C=)"
$atom:h12 $mol @atom:144 0.0 -1.23422 0.85446 0.0 #144->"alkene H (H-C=)"
$atom:h21 $mol @atom:144 0.0 1.23422 -0.85446 0.0 #144->"alkene H (H-C=)"
$atom:h22 $mol @atom:144 0.0 1.23422 0.85446 0.0 #144->"alkene H (H-C=)"
$atom:c1 $mol @atom:143 0.0 -0.6695 0.00000 0.0 #143->"C - CM | alkene C (H2-C=)"
$atom:c2 $mol @atom:143 0.0 0.6695 0.00000 0.0 #143->"C - CM | alkene C (H2-C=)"
$atom:h11 $mol @atom:144 0.0 -1.23422 -0.85446 0.0 #144->"H - HC | alkene H (H-C=)"
$atom:h12 $mol @atom:144 0.0 -1.23422 0.85446 0.0 #144->"H - HC | alkene H (H-C=)"
$atom:h21 $mol @atom:144 0.0 1.23422 -0.85446 0.0 #144->"H - HC | alkene H (H-C=)"
$atom:h22 $mol @atom:144 0.0 1.23422 0.85446 0.0 #144->"H - HC | alkene H (H-C=)"
}

# Note: You don't have to specify the charge in this example because we are
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