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Add setup_abfe and analyze_dhdl functionalities #28

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dccd63d
Modifications to setup_abfe and analyze_dhdl
lmacaya Aug 25, 2022
b35827c
Fix default salt concentration
lmacaya Aug 25, 2022
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4 changes: 2 additions & 2 deletions src/pmx/analysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -371,7 +371,7 @@ def smooth(x, window_len=11, window='hanning'):
print("Plotting: no smoothing for Wr")
plt.legend(shadow=True, fancybox=True, loc='upper center',
prop={'size': 12})
plt.ylabel(r'W [kJ/mol]', fontsize=20)
plt.ylabel(f'W [{units}]', fontsize=20)
plt.xlabel(r'# Snapshot', fontsize=20)
plt.grid(lw=2)
plt.xlim(0, x[-1]+1)
Expand All @@ -384,7 +384,7 @@ def smooth(x, window_len=11, window='hanning'):
plt.hist(wr, bins=nbins, orientation='horizontal', facecolor='blue',
alpha=.75, density=True)

x = np.arange(mini, maxi, .5)
x = np.arange(mini, maxi, .05)

y1 = gauss_func(Af, mf, devf, x)
y2 = gauss_func(Ab, mb, devb, x)
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2 changes: 1 addition & 1 deletion src/pmx/gmx.py
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Expand Up @@ -13,7 +13,7 @@
def get_gmx():
"""Gets path to gmx executable, and throws error if not found.
"""
gmx = which('gmx')
gmx = which('gmx_mpi') if which('gmx') is None else which('gmx')
if gmx is not None:
return gmx
else:
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2 changes: 2 additions & 0 deletions src/pmx/scripts/analyze_dhdl.py
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Expand Up @@ -618,6 +618,8 @@ def main(args):
# plot work distributions
# -----------------------
if args.wplot.lower() != 'none':
res_ab = [i * unit_fact for i in res_ab]
res_ba = [i * unit_fact for i in res_ba]
if quiet is False:
print('\n Plotting histograms......')
# hierarchy of estimators: BAR > Crooks > Jarz
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35 changes: 28 additions & 7 deletions src/pmx/scripts/setup_abfe.py
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Expand Up @@ -120,7 +120,25 @@ def parse_options():
'behaviour, provide a random seed.',
default=None,
type=int)

parser.add_argument('--conc',
metavar='float',
dest='conc',
help='Specify salt concentration (mol/liter). '
'Default is no salt added.',
default=0,
type=float)
parser.add_argument('--pname',
metavar='pname',
dest='pname',
help='Name of the positive ion. '
'Default is NA.',
default='NA')
parser.add_argument('--nname',
metavar='nname',
dest='nname',
help='Name of the negative ion. '
'Default is CL.',
default='CL')
args, unknown = parser.parse_known_args()
check_unknown_cmd(unknown)

Expand Down Expand Up @@ -250,8 +268,9 @@ def main(args):
# -----------------
gmx.solvate(cp='doublebox.gro', cs='spc216.gro', p='doublebox.top', o='solvate.gro')
gmx.write_mdp(mdp='enmin', fout='genion.mdp')
gmx.grompp(f='genion.mdp', c='solvate.gro', p='doublebox.top', o='genion.tpr', maxwarn=1)
gmx.genion(s='genion.tpr', p='doublebox.top', o='genion.gro', conc=0.15, neutral=True)
gmx.grompp(f='genion.mdp', c='solvate.gro', p='doublebox.top', o='genion.tpr', maxwarn=10)
gmx.genion(s='genion.tpr', p='doublebox.top', o='genion.gro', conc=args.conc, neutral=True,
other_flags=f'-pname {args.pname} -nname {args.nname}')

# add restraints to topology
doubletop = Topology('doublebox.top', assign_types=False)
Expand All @@ -276,8 +295,9 @@ def main(args):
gmx.editconf(f='complex.gro', o='editconf.gro', bt='cubic', d=1.2)
gmx.solvate(cp='editconf.gro', cs='spc216.gro', p='complex.top', o='solvate.gro')
gmx.write_mdp(mdp='enmin', fout='genion.mdp')
gmx.grompp(f='genion.mdp', c='solvate.gro', p='complex.top', o='genion.tpr', maxwarn=1)
gmx.genion(s='genion.tpr', p='complex.top', o='genion.gro', conc=0.15, neutral=True)
gmx.grompp(f='genion.mdp', c='solvate.gro', p='complex.top', o='genion.tpr', maxwarn=10)
gmx.genion(s='genion.tpr', p='complex.top', o='genion.gro', conc=args.conc, neutral=True,
other_flags=f'-pname {args.pname} -nname {args.nname}')

# add restraints to topology
comtop = Topology('complex.top', assign_types=False)
Expand Down Expand Up @@ -314,8 +334,9 @@ def main(args):
gmx.editconf(f='ligand.gro', o='editconf.gro', bt='cubic', d=1.2)
gmx.solvate(cp='editconf.gro', cs='spc216.gro', p='ligand.top', o='solvate.gro')
gmx.write_mdp(mdp='enmin', fout='genion.mdp')
gmx.grompp(f='genion.mdp', c='solvate.gro', p='ligand.top', o='genion.tpr', maxwarn=1)
gmx.genion(s='genion.tpr', p='ligand.top', o='genion.gro', conc=0.15, neutral=True)
gmx.grompp(f='genion.mdp', c='solvate.gro', p='ligand.top', o='genion.tpr', maxwarn=10)
gmx.genion(s='genion.tpr', p='ligand.top', o='genion.gro', conc=args.conc, neutral=True,
other_flags=f'-pname {args.pname} -nname {args.nname}')

os.chdir('../')

Expand Down