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added pop bespoke FF
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tlfobe authored and tlfobe committed Oct 7, 2024
1 parent 30a4f69 commit 28f0a42
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2 changes: 1 addition & 1 deletion simulations/terphenyl_pmp/tetramer_remd/t_250_450/bespoke/pmp_tetramer.build
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Expand Up @@ -5,5 +5,5 @@ lower_connect : 42
residue_name : PMP
cap_smiles : {upper : CO, lower : CC(C)(C)OC=O}
foldamer_length : 4
system : {solvent : TCM, solvent_smile_str : CCl, n_solvent : 634, box_size : 55.4}
system : {solvent : TCM, solvent_smile_str : ClC(Cl)Cl, n_solvent : 634, box_size : 55.4}
ff_method : bespoke-foldamer
9 changes: 9 additions & 0 deletions simulations/terphenyl_pop/tetramer_remd/t_250_450/bespoke/pop_tetramer.build
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structure_file : pop_tetramer
foldamer_smile : C(=O)c1ccc(c2c(cc(OC)cc2)(c3ccc(cc3)[C@@H](N)C))cc1
upper_connect : 25
lower_connect : 40
residue_name : POP
cap_smiles : {upper : CO, lower : CC(C)(C)OC=O}
foldamer_length : 4
system : {solvent : TCM, solvent_smile_str : ClC(Cl)Cl, n_solvent : 634, box_size : 55.4}
ff_method : bespoke-foldamer
12 changes: 12 additions & 0 deletions simulations/terphenyl_pop/tetramer_remd/t_250_450/bespoke/remd_parameters.yml
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simulation_id : pop_tetramer_bespoke_hmr
n_replicas : 64
t_range : [250, 450]
mdps :
- berendsen_nvt.mdp
- berendsen_npt.mdp
- production_npt.mdp
sim_id : sim
build_foldamer : pop_tetramer.build
param_method : bespoke
n_simulations : 3
gromacs_exe : gmx
319 changes: 319 additions & 0 deletions ...imulations/data/topology_manager/3582fb6e387e57e1aaa4f40f9e958ac2/molecule/pop_trimer.mol
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pop_trimer.pdb
OpenBabel10062412273D

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M END
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