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Merge pull request #24 from GOMC-WSU/addMosDef
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add mosdef examples
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@GregorySchwing
GregorySchwing authored Jun 24, 2022
2 parents 7fc1c5f + e25518c commit 4690d50
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661 changes: 661 additions & 0 deletions MoSDef-GOMC/LICENSE
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47 changes: 47 additions & 0 deletions MoSDef-GOMC/Part_1_GOMC_MoSDeF_overview/GEMC_NVT_Example_n_pentane_FF.py
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import mbuild as mb
import numpy as np
from foyer import Forcefield
import mbuild.formats.charmm_writer as mf_charmm
import mbuild.formats.gomc_conf_writer as gomc_control


# set the force field and create the all-atom (AA) pentane molecule via a smiles string
pentane = mb.load('CCCCC', smiles=True)
pentane.name = 'PEN'


# create the liquid and vapor boxes
box_liq = mb.fill_box(compound = [pentane],
n_compounds=[574],
box = [4.5, 4.5, 4.5])

box_vap = mb.fill_box(compound = [pentane],
n_compounds=[105],
box = [8.0, 8.0, 8.0])


# build the MoSDeF Charmm object
charmm = mf_charmm.Charmm(box_liq,
'GEMC_NVT_n_pentane_liq',
structure_box_1=box_vap,
filename_box_1='GEMC_NVT_n_pentane_vap',
ff_filename="GEMC_NVT_n_pentane_FF",
forcefield_selection='oplsaa',
residues=[pentane.name],
bead_to_atom_name_dict=None,
gomc_fix_bonds_angles=None,
)

# write the pdb, psf, and inp (parameter/force field) files
charmm.write_inp()
charmm.write_psf()
charmm.write_pdb()

# create the GOMC control file
gomc_control.write_gomc_control_file(charmm, 'in_GEMC_NVT.conf', 'GEMC_NVT', 100, 300,
input_variables_dict={"Potential" : 'SWITCH',
"Rswitch" : 10,
"Rcut": 12,
"RcutLow": 1,
"VDWGeometricSigma": True})

3 changes: 3 additions & 0 deletions MoSDef-GOMC/Part_1_GOMC_MoSDeF_overview/README.md
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# Constructing and Executing GOMC Simulations via MoSDeF

[![IMAGE ALT TEXT](play.png)](https://www.youtube.com/watch?v=7StVoUCGkHs "GOMC videos part 1a: Constructing and Executing GOMC Simulations via MoSDeF")
11 changes: 11 additions & 0 deletions MoSDef-GOMC/Part_1_GOMC_MoSDeF_overview/output_example/Blk_Output_data_BOX_0.dat
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#STEPS TOT_EN EN_INTER EN_TC EN_INTRA(B) EN_INTRA(NB) EN_ELECT EN_REAL EN_RECIP TOTAL_VIR PRESSURE TOT_DENS VOLUME HEAT_VAP
10 4.20201869e+06 2.84334411e+06 0.00000000e+00 7.05433128e+05 6.74589378e+05 -2.13479179e+04 9.98852301e+03 1.50892658e+04 1.47145561e+08 7.45750761e+04 7.54662232e+02 9.11250000e+04 -3.99049327e+01
20 4.20197757e+06 2.84321411e+06 0.00000000e+00 7.05502986e+05 6.74607758e+05 -2.13472778e+04 9.98858216e+03 1.50893575e+04 1.47108521e+08 7.45563697e+04 7.54662232e+02 9.11250000e+04 -3.98648477e+01
30 4.19407825e+06 2.83531489e+06 0.00000000e+00 7.05790237e+05 6.74267949e+05 -2.12948253e+04 1.00082859e+04 1.50980658e+04 1.46989197e+08 7.44960613e+04 7.54267809e+02 9.11250000e+04 -3.95335409e+01
40 4.17162579e+06 2.80832720e+06 0.00000000e+00 7.10838688e+05 6.73559501e+05 -2.10995989e+04 1.01478509e+04 1.50991864e+04 1.45910804e+08 7.39510221e+04 7.53347489e+02 9.11250000e+04 -3.87666247e+01
50 4.14986976e+06 2.78862518e+06 0.00000000e+00 7.09732278e+05 6.72502616e+05 -2.09903138e+04 1.01479798e+04 1.51355476e+04 1.45780644e+08 7.38852407e+04 7.52164221e+02 9.11250000e+04 -3.86925258e+01
60 4.14741753e+06 2.78639923e+06 0.00000000e+00 7.09610587e+05 6.72385228e+05 -2.09775146e+04 1.01486230e+04 1.51396153e+04 1.44971867e+08 7.34763682e+04 7.52032747e+02 9.11250000e+04 -3.81163689e+01
70 4.12643729e+06 2.76849856e+06 0.00000000e+00 7.08008741e+05 6.70858635e+05 -2.09286504e+04 1.00428888e+04 1.51890587e+04 1.44826189e+08 7.34027041e+04 7.50323582e+02 9.11250000e+04 -3.79829325e+01
80 4.10427088e+06 2.74931331e+06 0.00000000e+00 7.06412484e+05 6.69331656e+05 -2.07865683e+04 1.00525409e+04 1.52163292e+04 1.43479288e+08 7.27216037e+04 7.48614416e+02 9.11250000e+04 -3.66441710e+01
90 4.09556196e+06 2.74148421e+06 0.00000000e+00 7.05921396e+05 6.68861542e+05 -2.07051833e+04 1.01041384e+04 1.52137586e+04 1.42927364e+08 7.24424517e+04 7.48088519e+02 9.11250000e+04 -3.60105637e+01
100 4.09514594e+06 2.74107674e+06 0.00000000e+00 7.05921396e+05 6.68861542e+05 -2.07137375e+04 1.00968693e+04 1.52124735e+04 1.42889428e+08 7.24232927e+04 7.48088519e+02 9.11250000e+04 -3.57117326e+01
11 changes: 11 additions & 0 deletions MoSDef-GOMC/Part_1_GOMC_MoSDeF_overview/output_example/Blk_Output_data_BOX_1.dat
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#STEPS TOT_EN EN_INTER EN_TC EN_INTRA(B) EN_INTRA(NB) EN_ELECT EN_REAL EN_RECIP TOTAL_VIR PRESSURE TOT_DENS VOLUME HEAT_VAP
10 2.44921479e+05 -7.34060072e+03 0.00000000e+00 1.28914820e+05 1.23363773e+05 -1.65137430e+01 2.06773179e+02 8.26944391e+03 -3.29233674e+04 5.53487736e+00 2.45695727e+01 5.12000000e+05 -3.99049327e+01
20 2.45008640e+05 -7.36492011e+03 0.00000000e+00 1.29030663e+05 1.23361457e+05 -1.85604856e+01 2.05025381e+02 8.26897960e+03 -3.17896467e+04 5.63678298e+00 2.45695727e+01 5.12000000e+05 -3.98648477e+01
30 2.47431025e+05 -7.80498341e+03 0.00000000e+00 1.31629916e+05 1.23639440e+05 -3.33477401e+01 1.97842134e+02 8.29087588e+03 -2.17526423e+04 6.54705892e+00 2.46397714e+01 5.12000000e+05 -3.95335409e+01
40 2.53651826e+05 -7.84070125e+03 0.00000000e+00 1.37281092e+05 1.24244271e+05 -3.28365071e+01 1.99758865e+02 8.35836155e+03 -2.12270656e+04 6.66710857e+00 2.48035686e+01 5.12000000e+05 -3.87666247e+01
50 2.61044287e+05 -8.13072951e+03 0.00000000e+00 1.43665659e+05 1.25540930e+05 -3.15728580e+01 2.13910578e+02 8.42520901e+03 -2.14446745e+04 6.65563832e+00 2.50141649e+01 5.12000000e+05 -3.86925258e+01
60 2.61837699e+05 -8.19048248e+03 0.00000000e+00 1.44375697e+05 1.25685287e+05 -3.28023319e+01 2.11980374e+02 8.43475960e+03 -2.35140302e+04 6.54243988e+00 2.50375645e+01 5.12000000e+05 -3.81163689e+01
70 2.73623977e+05 -8.81734431e+03 0.00000000e+00 1.55260519e+05 1.27211473e+05 -3.06707696e+01 2.30320843e+02 8.52961967e+03 -2.31154062e+04 6.59445007e+00 2.53417592e+01 5.12000000e+05 -3.79829325e+01
80 2.84740661e+05 -9.57374923e+03 0.00000000e+00 1.65292608e+05 1.29050568e+05 -2.87669644e+01 2.42817630e+02 8.62313972e+03 -1.71730396e+04 7.28229072e+00 2.56459539e+01 5.12000000e+05 -3.66441710e+01
90 2.88650918e+05 -1.00964260e+04 0.00000000e+00 1.69067142e+05 1.29708029e+05 -2.78265471e+01 2.59801774e+02 8.64293164e+03 -1.37581532e+04 7.66204886e+00 2.57395523e+01 5.12000000e+05 -3.60105637e+01
100 2.89491325e+05 -1.03386926e+04 0.00000000e+00 1.70228269e+05 1.29629091e+05 -2.73427944e+01 2.67934829e+02 8.64061929e+03 -6.82623569e+03 8.28513122e+00 2.57395523e+01 5.12000000e+05 -3.57117326e+01
122 changes: 122 additions & 0 deletions MoSDef-GOMC/Part_1_GOMC_MoSDeF_overview/output_example/GEMC_NVT_n_pentane_FF.inp
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* GEMC_NVT_n_pentane_liq and GEMC_NVT_n_pentane_vap - created by mBuild using the on 2021-04-20 11:56:45.482364
* parameters from the {'PEN': 'oplsaa'} force field(s) via MoSDef
* 1-4 coulombic scaling = {'PEN': 0.5}, and 1-4 LJ scaling = {'PEN': 0.5}

* 11543 atoms
* 10864 bonds
* 20370 angles
* 24444 dihedrals
* 0 impropers

* 3 atom types
* 4 bond types
* 7 angle types
* 7 dihedral types


* masses

! atom_types mass atomTypeForceFieldName_ResidueName (i.e., atoms_type_per_utilized_FF)
* A 12.010780 ! opls_135_PEN
* B 12.010780 ! opls_136_PEN
* C 1.007947 ! opls_140_PEN

BONDS * harmonic
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!Kb (kcal/mol) = Kb_K (K) * Boltz. const.; (9999999999 if no stretching)
!
!atom_types Kb b0 atoms_types_per_utilized_FF
B B 268.0 1.529 ! opls_136_PEN opls_136_PEN
A C 340.0 1.09 ! opls_135_PEN opls_140_PEN
A B 268.0 1.529 ! opls_135_PEN opls_136_PEN
B C 340.0 1.09 ! opls_136_PEN opls_140_PEN

ANGLES * harmonic
!
!V(angle) = Ktheta(Theta - Theta0)**2
!
!Ktheta: kcal/mole/rad**2
!Theta0: degrees
!
! Ktheta (kcal/mol) = Ktheta_K (K) * Boltz. const.
!
!atom_types Ktheta Theta0 atoms_types_per_utilized_FF
C A C 33.0 107.80000 ! opls_140_PEN opls_135_PEN opls_140_PEN
A B C 37.5 110.70000 ! opls_135_PEN opls_136_PEN opls_140_PEN
A B B 58.3500239 112.70000 ! opls_135_PEN opls_136_PEN opls_136_PEN
B A C 37.5 110.70000 ! opls_136_PEN opls_135_PEN opls_140_PEN
B B C 37.5 110.70000 ! opls_136_PEN opls_136_PEN opls_140_PEN
B B B 58.3500239 112.70000 ! opls_136_PEN opls_136_PEN opls_136_PEN
C B C 33.0 107.80000 ! opls_140_PEN opls_136_PEN opls_140_PEN

DIHEDRALS * CHARMM
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
! Kchi (kcal/mol) = Kchi_K (K) * Boltz. const.
! Boltzmann = 0.0019872041 kcal / (mol * K)
!
!atom_types Kchi n delta atoms_types_per_utilized_FF
B B A C 0.300000 0 90.0 ! opls_136_PEN opls_136_PEN opls_135_PEN opls_140_PEN
B B A C 0.000000 1 180.0 ! opls_136_PEN opls_136_PEN opls_135_PEN opls_140_PEN
B B A C 0.000000 2 0.0 ! opls_136_PEN opls_136_PEN opls_135_PEN opls_140_PEN
B B A C -0.150000 3 180.0 ! opls_136_PEN opls_136_PEN opls_135_PEN opls_140_PEN
B B A C 0.000000 4 0.0 ! opls_136_PEN opls_136_PEN opls_135_PEN opls_140_PEN
B B A C 0.000000 5 180.0 ! opls_136_PEN opls_136_PEN opls_135_PEN opls_140_PEN
C A B C 0.300000 0 90.0 ! opls_140_PEN opls_135_PEN opls_136_PEN opls_140_PEN
C A B C 0.000000 1 180.0 ! opls_140_PEN opls_135_PEN opls_136_PEN opls_140_PEN
C A B C 0.000000 2 0.0 ! opls_140_PEN opls_135_PEN opls_136_PEN opls_140_PEN
C A B C -0.150000 3 180.0 ! opls_140_PEN opls_135_PEN opls_136_PEN opls_140_PEN
C A B C 0.000000 4 0.0 ! opls_140_PEN opls_135_PEN opls_136_PEN opls_140_PEN
C A B C 0.000000 5 180.0 ! opls_140_PEN opls_135_PEN opls_136_PEN opls_140_PEN
B B B C 0.300000 0 90.0 ! opls_136_PEN opls_136_PEN opls_136_PEN opls_140_PEN
B B B C 0.000000 1 180.0 ! opls_136_PEN opls_136_PEN opls_136_PEN opls_140_PEN
B B B C 0.000000 2 0.0 ! opls_136_PEN opls_136_PEN opls_136_PEN opls_140_PEN
B B B C -0.150000 3 180.0 ! opls_136_PEN opls_136_PEN opls_136_PEN opls_140_PEN
B B B C 0.000000 4 0.0 ! opls_136_PEN opls_136_PEN opls_136_PEN opls_140_PEN
B B B C 0.000000 5 180.0 ! opls_136_PEN opls_136_PEN opls_136_PEN opls_140_PEN
C B A C 0.300000 0 90.0 ! opls_140_PEN opls_136_PEN opls_135_PEN opls_140_PEN
C B A C 0.000000 1 180.0 ! opls_140_PEN opls_136_PEN opls_135_PEN opls_140_PEN
C B A C 0.000000 2 0.0 ! opls_140_PEN opls_136_PEN opls_135_PEN opls_140_PEN
C B A C -0.150000 3 180.0 ! opls_140_PEN opls_136_PEN opls_135_PEN opls_140_PEN
C B A C 0.000000 4 0.0 ! opls_140_PEN opls_136_PEN opls_135_PEN opls_140_PEN
C B A C 0.000000 5 180.0 ! opls_140_PEN opls_136_PEN opls_135_PEN opls_140_PEN
A B B B 1.450000 0 90.0 ! opls_135_PEN opls_136_PEN opls_136_PEN opls_136_PEN
A B B B -0.650000 1 180.0 ! opls_135_PEN opls_136_PEN opls_136_PEN opls_136_PEN
A B B B 0.025000 2 0.0 ! opls_135_PEN opls_136_PEN opls_136_PEN opls_136_PEN
A B B B -0.100000 3 180.0 ! opls_135_PEN opls_136_PEN opls_136_PEN opls_136_PEN
A B B B 0.000000 4 0.0 ! opls_135_PEN opls_136_PEN opls_136_PEN opls_136_PEN
A B B B 0.000000 5 180.0 ! opls_135_PEN opls_136_PEN opls_136_PEN opls_136_PEN
A B B C 0.300000 0 90.0 ! opls_135_PEN opls_136_PEN opls_136_PEN opls_140_PEN
A B B C 0.000000 1 180.0 ! opls_135_PEN opls_136_PEN opls_136_PEN opls_140_PEN
A B B C 0.000000 2 0.0 ! opls_135_PEN opls_136_PEN opls_136_PEN opls_140_PEN
A B B C -0.150000 3 180.0 ! opls_135_PEN opls_136_PEN opls_136_PEN opls_140_PEN
A B B C 0.000000 4 0.0 ! opls_135_PEN opls_136_PEN opls_136_PEN opls_140_PEN
A B B C 0.000000 5 180.0 ! opls_135_PEN opls_136_PEN opls_136_PEN opls_140_PEN
C B B C 0.300000 0 90.0 ! opls_140_PEN opls_136_PEN opls_136_PEN opls_140_PEN
C B B C 0.000000 1 180.0 ! opls_140_PEN opls_136_PEN opls_136_PEN opls_140_PEN
C B B C 0.000000 2 0.0 ! opls_140_PEN opls_136_PEN opls_136_PEN opls_140_PEN
C B B C -0.150000 3 180.0 ! opls_140_PEN opls_136_PEN opls_136_PEN opls_140_PEN
C B B C 0.000000 4 0.0 ! opls_140_PEN opls_136_PEN opls_136_PEN opls_140_PEN
C B B C 0.000000 5 180.0 ! opls_140_PEN opls_136_PEN opls_136_PEN opls_140_PEN
! RB-torsion to CHARMM dihedral conversion error is OK [error <= 10^(-10)]
! Maximum( |(RB-torsion calc)-(CHARMM dihedral calc)| ) = 1.3322676295501878e-15

NONBONDED
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!atype ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 atom_type_per_utilized_FF
A 0.00 -0.066000000 1.96430858454 0.00 -0.033000000 1.96430858454 ! opls_135_PEN opls_135_PEN
B 0.00 -0.066000000 1.96430858454 0.00 -0.033000000 1.96430858454 ! opls_136_PEN opls_136_PEN
C 0.00 -0.030000000 1.40307756039 0.00 -0.015000000 1.40307756039 ! opls_140_PEN opls_140_PEN

END
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