Source code for adaptivemastermsm.launcher.launcher_lib
"""
This file is part of the AdaptiveMasterMSM package.
"""
#!/usr/bin/env python
import sys, os
[docs]def checkfile(inp):
if not os.path.exists(inp[:inp.rfind("/")]):
os.makedirs(inp[:inp.rfind("/")])
#def clean_working_directory():
#
# print ("Cleaning up...")
# os.system('rm \#*')
# os.system('mkdir logs')
# os.system('mv *.log logs')
# os.system('rm *.trr *.top *.itp *.edr *.cpt *.tpr out.gro conf.gro')
# os.system('mv equilibration.xtc *.mdp *.gro logs')
[docs]def write_mdp_min(emstep=0.001, nsteps=50000, constraints="none"):
txt = """
; GROMACS mdp minimization options
integrator = steep
emstep = %f
emtol = 10.0
nsteps = %d
nstxout = 0
nstvout = 0
nstlog = 1000
nstenergy = 0
nstxtcout = 0
xtc_grps = System
energygrps =
nstlist = 1
ns_type = grid
pbc = xyz
periodic_molecules = no
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
tcoupl = no
Pcoupl = no
gen_vel = yes
constraints = %s
continuation = no
morse = no
implicit_solvent = no
""" % (emstep, nsteps, constraints)
return txt
[docs]def write_mdp_nvt(dt=0.002, nsteps=50000, constraints="h-bonds", ref_t=300):
txt = """
define = -DPOSRES
integrator = md
dt = %f ; ps
nsteps = %d ; 100 ps
nstlog = 1000
nstenergy = 1000
nstxout-compressed = 1000
constraint_algorithm = lincs
constraints = %s
lincs_iter = 1
lincs_order = 4
nstlist = 10
ns_type = grid
cutoff-scheme = verlet
coulombtype = pme
rvdw = 1.
rcoulomb = 1.
;# with PME we should not have to use coupling groups
tcoupl = v-rescale
tc_grps = protein non-protein
tau_t = 0.1 0.1
ref_t = %d %d
Pcoupl = no
pbc = xyz
gen_vel = yes
gen_temp = 10.0
gen_seed = -1
""" % (dt, nsteps, constraints, ref_t, ref_t)
return txt
[docs]def write_mdp_npt(dt=0.002, nsteps=50000, constraints="h-bonds",\
ref_t=300, ref_p=1.0):
txt = """
refcoord_scaling = com
integrator = md
dt = %f
nsteps = %d
nstlog = 1000
nstenergy = 1000
nstxout-compressed = 1000
compressed-x-grps = non-Water
continuation = yes
constraint_algorithm = lincs
constraints = %s
lincs_iter = 1
lincs_order = 4
cutoff-scheme = verlet
nstlist = 10
ns_type = grid
coulombtype = pme
pme_order = 4
fourier_spacing = 0.16
rvdw = 1.
rcoulomb = 1.
tcoupl = v-rescale
tc_grps = protein non-protein
tau_t = 0.1 0.1
ref_t = %d %d
; Isotropic pressure coupling is now on
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p = 2.0
ref_p = %f
compressibility = 4.5e-5
pbc = xyz
gen_vel = no
""" % (dt, nsteps, constraints, ref_t, ref_t, ref_p)
return txt
[docs]def write_mdp_prod(emstep=0.002, nsteps=50000, constraints="h-bonds"):
txt = """
; GROMACS mdp production options
integrator = sd
dt = %f ; in ps
nsteps = %d
nstlog = 100
nstenergy = 100
nstxout-compressed = 100
; nstxtcout = 100
; xtc-grps = protein
compressed-x-grps = non-Water
continuation = yes
constraint_algorithm = lincs
constraints = %s
lincs_iter = 1
lincs_order = 4
nstlist = 10
ns_type = grid
cutoff-scheme = verlet
coulombtype = pme
rvdw = 1.
rcoulomb = 1.
tc_grps = protein non-protein
tau_t = 1 1
ref_t = 300.0 300.0
Pcoupl = no
gen_vel = no
""" % (emstep, nsteps, constraints)
return txt
#integrator = md
#dt = 0.004
#nsteps = 150000000 ; 600ns
#nstlog = 2500
#nstxout = 2500
#nstvout = 2500
#nstfout = 2500
#nstcalcenergy = 2500
#nstenergy = 2500
#;energygrps = Protein Non-Protein ; Not available for GPU-based runs
#;
#cutoff-scheme = Verlet
#nstlist = 20
#coulombtype = pme
#rcoulomb = 1.2
#vdwtype = Cut-off
#vdw-modifier = Force-switch
#rvdw_switch = 1.0
#rvdw = 1.2
#;
#tcoupl = V-rescale
#tc_grps = Protein Non-Protein
#tau_t = 0.1 0.1
#ref_t = 310 310
#nsttcouple = 10
#;
#pcoupl = Parrinello-Rahman
#pcoupltype = isotropic
#tau_p = 2.0
#compressibility = 4.5e-5
#ref_p = 1.0
#;
#constraints = all-bonds
#constraint_algorithm = LINCS
#continuation = yes
#;
#refcoord_scaling = com
#DispCorr = EnerPres
#gen-vel = no ; Assign velocities to particles by taking them randomly from a Maxwell distributioni
#gen-temp = 310
#def write_mdp_user(params):
#
# txt = """; GROMACS mdp options
# ; Run parameters
# integrator = md
# dt = %f
# ; Output control
# nsteps = %d
# nstxout = 0
# nstvout = 0
# nstlog = %d
# nstenergy = 0
# nstxout-compressed = %d
# compressed-x-grps = System
# ; Neighbors
# cutoff-scheme = Verlet ; Buffered neighbor searching
# ns_type = grid ; search neighboring grid cells
# rvdw = 0.1
# ; rvdw_switch = 1.0
# pbc = xyz
# rlist = 0.03
# nstlist = 10
# ; Electrostatics
# coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
# rcoulomb = 0.1 ; short-range electrostatic cutoff (in nm)
# ; fourier_nx = 0
# ; fourier_ny = 0
# ; fourier_nz = 0
# ; optimize_fft = yes
# pme_order = 4 ; cubic interpolation
# fourierspacing = 0.08 ; grid spacing for FFT
# DispCorr = EnerPres ; account for cut-off vdW scheme
# ; T and P coupling
# tcoupl = %s
# tc_grps = System
# ; tc_grps = Protein Non-Protein ; two coupling groups-more accurate
# tau_t = 0.1
# ref_t = %f
# pcoupl = %s
# tau_p = 1
# ref_p = %f
# pcoupltype = isotropic
# compressibility = 0.000045
# ; Bond parameters
# gen_vel = no
# gen_temp = %f
# constraint_algorithm = lincs ; holonomic constraints
# constraints = h-bonds ; bonds involving H are constrained
# lincs_iter = 1 ; accuracy of LINCS
# lincs_order = 4 ; also related to accoutput
# continuation = yes
# morse = no
# implicit_solvent = no
# """ % ( params['timestep'],
# params['total_steps'],
# params['log_freq'],
# params['xtc_freq'],
# params['thermostat'],
# params['temperature'],
# params['barostat'],
# params['pressure'],
# params['temperature'] )
#
# return txt
#
