def equilibrate(groups=None,structure='system'):
"""
equilibrate()
Standard equilibration procedure.
"""
#---sequential equilibration stages
seq = wordspace.equilibration.split(',') if wordspace.equilibration else []
for eqnum,name in enumerate(seq):
if not equilibrate_check(name):
gmx('grompp',base='md-%s'%name,top='system',
structure=structure if eqnum == 0 else 'md-%s'%seq[eqnum-1],
log='grompp-%s'%name,mdp='input-md-%s-eq-in'%name,
flag=('' if not groups else '-n %s'%groups)+' -maxwarn 10')
gmx('mdrun',base='md-%s'%name,log='mdrun-%s'%name,skip=True)
assert os.path.isfile(wordspace['step']+'md-%s.gro'%name)
checkpoint()
#---first part of the equilibration/production run
name = 'md.part0001'
if not equilibrate_check(name) or seq == []:
gmx('grompp',base=name,top='system',
structure='md-%s'%seq[-1] if seq else structure,
log='grompp-0001',mdp='input-md-in',
flag='' if not groups else '-n %s'%groups)
gmx('mdrun',base=name,log='mdrun-0001')
#---we don't assert that the file exists here because the user might kill it and upload
checkpoint()
def minimize_steep_cg(name):
"""
minimize_steep_cg(name)
Minimization using steepest descent followed by conjugate gradient.
Note that this method has been retired due to reliability issues.
"""
gmx('grompp',
base='em-%s-steep' % name,
top=name,
structure=name,
log='grompp-em-%s-steep' % name,
mdp='input-em-steep-in')
gmx('mdrun',
base='em-%s-steep' % name,
log='mdrun-%s-steep' % name,
skip=True)
#---if first step fails we skip it and try again with the second minimizer
if not os.path.isfile(wordspace['step'] + 'em-%s-steep.gro'):
filecopy(wordspace['step'] + '%s.gro' % name,
wordspace['step'] + 'em-%s-steep.gro' % name)
gmx('grompp',
base='em-%s-cg' % name,
top=name,
structure='em-%s-steep' % name,
log='grompp-%s-cg' % name,
mdp='input-em-cg-in',
skip=True)
gmx('mdrun', base='em-%s-cg' % name, log='mdrun-%s-cg' % name)
select_minimum('%s-steep' % name,
'%s-cg' % name,
gro='%s-minimized' % name)
checkpoint()
def equilibrate(groups=None, structure='system'):
"""
equilibrate()
Standard equilibration procedure.
"""
#---sequential equilibration stages
seq = wordspace.equilibration.split(',') if wordspace.equilibration else []
for eqnum, name in enumerate(seq):
if not equilibrate_check(name):
gmx('grompp',
base='md-%s' % name,
top='system',
structure=structure if eqnum == 0 else 'md-%s' %
seq[eqnum - 1],
log='grompp-%s' % name,
mdp='input-md-%s-eq-in' % name,
flag=('' if not groups else '-n %s' % groups) + ' -maxwarn 10')
gmx('mdrun', base='md-%s' % name, log='mdrun-%s' % name, skip=True)
assert os.path.isfile(wordspace['step'] + 'md-%s.gro' % name)
checkpoint()
#---first part of the equilibration/production run
name = 'md.part0001'
if not equilibrate_check(name) or seq == []:
gmx('grompp',
base=name,
top='system',
structure='md-%s' % seq[-1] if seq else structure,
log='grompp-0001',
mdp='input-md-in',
flag='' if not groups else '-n %s' % groups)
gmx('mdrun', base=name, log='mdrun-0001')
#---we don't assert that the file exists here because the user might kill it and upload
checkpoint()
def minimize(name,method='steep',top=None):
"""
minimize(name,method='steep')
Standard minimization procedure.
"""
gmx('grompp',base='em-%s-%s'%(name,method),top=name if not top else re.sub('^(.+)\.top$',r'\1',top),
structure=name,log='grompp-%s-%s'%(name,method),mdp='input-em-%s-in'%method,skip=True)
assert os.path.isfile(wordspace['step']+'em-%s-%s.tpr'%(name,method))
gmx('mdrun',base='em-%s-%s'%(name,method),log='mdrun-%s-%s'%(name,method))
filecopy(wordspace['step']+'em-'+'%s-%s.gro'%(name,method),
wordspace['step']+'%s-minimized.gro'%name)
checkpoint()
def minimize_steep_cg(name):
"""
minimize_steep_cg(name)
Minimization using steepest descent followed by conjugate gradient.
Note that this method has been retired due to reliability issues.
"""
gmx('grompp',base='em-%s-steep'%name,top=name,structure=name,
log='grompp-em-%s-steep'%name,mdp='input-em-steep-in')
gmx('mdrun',base='em-%s-steep'%name,log='mdrun-%s-steep'%name,skip=True)
#---if first step fails we skip it and try again with the second minimizer
if not os.path.isfile(wordspace['step']+'em-%s-steep.gro'):
filecopy(wordspace['step']+'%s.gro'%name,wordspace['step']+'em-%s-steep.gro'%name)
gmx('grompp',base='em-%s-cg'%name,top=name,structure='em-%s-steep'%name,
log='grompp-%s-cg'%name,mdp='input-em-cg-in',skip=True)
gmx('mdrun',base='em-%s-cg'%name,log='mdrun-%s-cg'%name)
select_minimum('%s-steep'%name,'%s-cg'%name,gro='%s-minimized'%name)
checkpoint()
def minimize(name, method='steep', top=None):
"""
minimize(name,method='steep')
Standard minimization procedure.
"""
gmx('grompp',
base='em-%s-%s' % (name, method),
top=name if not top else re.sub('^(.+)\.top$', r'\1', top),
structure=name,
log='grompp-%s-%s' % (name, method),
mdp='input-em-%s-in' % method,
skip=True)
assert os.path.isfile(wordspace['step'] + 'em-%s-%s.tpr' % (name, method))
gmx('mdrun',
base='em-%s-%s' % (name, method),
log='mdrun-%s-%s' % (name, method))
filecopy(wordspace['step'] + 'em-' + '%s-%s.gro' % (name, method),
wordspace['step'] + '%s-minimized.gro' % name)
checkpoint()