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Add TEMPO M3 model to the small molecule library [arXiv:2209.02072] #14

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Add TEMPO M3 model to the small molecule library [arXiv:2209.02072] #14

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1 change: 1 addition & 0 deletions new_models/SMILES/TEMPO.smiles
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
CC1(CCCC(N1[O])(C)C)C
36 changes: 36 additions & 0 deletions new_models/itps/cog-mono/TEMPO_cog.itp
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;;;;;; TEMPO (2,2,6,6-TETRAMETHYLPIPERIDINE-1-OXYL)
;
; Note(s):
; For minimizations, you may use define=-DFLEXIBLE to use a stiff-bond version of the topology that is more amenable to minimization.
;

[moleculetype]
; molname nrexcl
TEMPO 1

[atoms]
; id type resnr residu atom cgnr charge
1 TP5 1 TEMPO N1 1 0
2 SC3 1 TEMPO C2 2 0
3 SC3 1 TEMPO C3 3 0
4 SC3 1 TEMPO C4 4 0

[bonds]
2 4 1 0.378 25000 ; cog
3 4 1 0.378 25000 ; cog
#ifndef FLEXIBLE
[constraints]
#endif
; i j funct length
1 2 1 0.238 1000000 ; cog
1 3 1 0.238 1000000 ; cog
1 4 1 0.387 1000000 ; cog

[dihedrals]
; i j k l funct ref.angle force_k
1 2 3 4 2 180.00 10

[exclusions]
1 4

36 changes: 36 additions & 0 deletions new_models/itps/opt-mono/TEMPO.itp
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Original file line number Diff line number Diff line change
@@ -0,0 +1,36 @@

;;;;;; TEMPO (2,2,6,6-TETRAMETHYLPIPERIDINE-1-OXYL)
;
; Note(s):
; For minimizations, you may use define=-DFLEXIBLE to use a stiff-bond version of the topology that is more amenable to minimization.
;

[moleculetype]
; molname nrexcl
TEMPO 1

[atoms]
; id type resnr residu atom cgnr charge
1 TP5 1 TEMPO N1 1 0
2 SC3 1 TEMPO C2 2 0
3 SC3 1 TEMPO C3 3 0
4 SC3 1 TEMPO C4 4 0

[bonds]
2 4 1 0.378 25000 ; cog
3 4 1 0.378 25000 ; cog
#ifndef FLEXIBLE
[constraints]
#endif
; i j funct length
1 2 1 0.238 1000000 ; cog
1 3 1 0.238 1000000 ; cog
1 4 1 0.387 1000000 ; cog

[dihedrals]
; i j k l funct ref.angle force_k
1 2 3 4 2 180.00 10

[exclusions]
1 4