def MolecularDynamics(topology_file="ioned_topol",
input_structure="em",
output_name="t_0",
seed=1993,
steps=100,
pcoupling="semiisotropic"):
if debug_status:
replace_steps(configuration['mdp_files'] + "cg-mdrun-50ns_sts.mdp",
"runfile.mdp")
elif pcoupling == "semiisotropic":
replace_seed(configuration['mdp_files'] + "cg-mdrun-50ns_sts.mdp",
"seeded.mdp", seed)
replace_steps("seeded.mdp", "runfile.mdp", steps)
elif pcoupling == "anistropic":
replace_seed(configuration['mdp_files'] + "cg-mdrun-50ns_sts.mdp",
"seeded.mdp", seed)
replace_pcoupling("seeded.mdp",
"aniso_pcouple.mdp",
coupling="anisotropic")
replace_steps("aniso_pcouple.mdp", "runfile.mdp", steps)
#os.system(gromacs+"grompp -f runfile -c " + input_structure + " -p " + topology_file + " -o " + output_name + " >& grompp_" + output_name + ".log")
#os.system(gromacs+"mdrun -deffnm " + output_name)
UserDefSimulation(topology_file,
input_structure,
output_name,
"runfile.mdp",
wallclock=True)
def PRMolecularDynamics(topology_file="ioned_topol",input_structure="em",output_name="t_0",seed=1993,steps=100): if debug_status: replace_steps(configuration['mdp_files'] + "cg-pr.mdp","runfile.mdp") else: replace_seed(configuration['mdp_files'] + "cg-pr.mdp","runfile.mdp",seed) #os.system(gromacs+"grompp -f runfile -c " + input_structure + " -p " + topology_file + " -o " + output_name + " >& grompp_" + output_name + ".log") #os.system(gromacs+"mdrun -deffnm " + output_name) UserDefSimulation(topology_file,input_structure,output_name,"runfile.mdp")
def PMFMolecularDynamics(topology_file="ioned_topol",input_structure="pr",output_name="t_0",seed=1993,steps=2500000):
if debug_status:
replace_steps(configuration['mdp_files'] + "cg-mdrun-50ns_sts.mdp","runfile.mdp")
else:
replace_seed(configuration['mdp_files'] + "cg-mdrun-50ns_sts.mdp","seeded.mdp",seed)
replace_steps("seeded.mdp","runfile.mdp",steps)
os.system(gromacs+"grompp -f runfile -n pull_system.ndx -c " + input_structure + " -p " + topology_file + " -o " + output_name + " >& grompp_" + output_name + ".log")
os.system(gromacs+"mdrun -pi umbrella.ppa -po umbrella.gmx.ppa -pd pull.pdo -pn pull_system.ndx -deffnm " + output_name)
def MolecularDynamics(topology_file="ioned_topol",input_structure="em",output_name="t_0",seed=1993,steps=100,pcoupling="semiisotropic"):
if debug_status:
replace_steps(configuration['mdp_files'] + "cg-mdrun-50ns_sts.mdp","runfile.mdp")
elif pcoupling == "semiisotropic":
replace_seed(configuration['mdp_files'] + "cg-mdrun-50ns_sts.mdp","seeded.mdp",seed)
replace_steps("seeded.mdp","runfile.mdp",steps)
elif pcoupling == "anistropic":
replace_seed(configuration['mdp_files'] + "cg-mdrun-50ns_sts.mdp","seeded.mdp",seed)
replace_pcoupling("seeded.mdp","aniso_pcouple.mdp",coupling="anisotropic")
replace_steps("aniso_pcouple.mdp","runfile.mdp",steps)
#os.system(gromacs+"grompp -f runfile -c " + input_structure + " -p " + topology_file + " -o " + output_name + " >& grompp_" + output_name + ".log")
#os.system(gromacs+"mdrun -deffnm " + output_name)
UserDefSimulation(topology_file,input_structure,output_name,"runfile.mdp",wallclock=True)
def PRMolecularDynamics(topology_file="ioned_topol",
input_structure="em",
output_name="t_0",
seed=1993,
steps=100):
if debug_status:
replace_steps(configuration['mdp_files'] + "cg-pr.mdp", "runfile.mdp")
else:
replace_seed(configuration['mdp_files'] + "cg-pr.mdp", "runfile.mdp",
seed)
#os.system(gromacs+"grompp -f runfile -c " + input_structure + " -p " + topology_file + " -o " + output_name + " >& grompp_" + output_name + ".log")
#os.system(gromacs+"mdrun -deffnm " + output_name)
UserDefSimulation(topology_file, input_structure, output_name,
"runfile.mdp")
def PMFMolecularDynamics(topology_file="ioned_topol",
input_structure="pr",
output_name="t_0",
seed=1993,
steps=2500000):
if debug_status:
replace_steps(configuration['mdp_files'] + "cg-mdrun-50ns_sts.mdp",
"runfile.mdp")
else:
replace_seed(configuration['mdp_files'] + "cg-mdrun-50ns_sts.mdp",
"seeded.mdp", seed)
replace_steps("seeded.mdp", "runfile.mdp", steps)
os.system(gromacs + "grompp -f runfile -n pull_system.ndx -c " +
input_structure + " -p " + topology_file + " -o " + output_name +
" >& grompp_" + output_name + ".log")
os.system(
gromacs +
"mdrun -pi umbrella.ppa -po umbrella.gmx.ppa -pd pull.pdo -pn pull_system.ndx -deffnm "
+ output_name)
def RobustMolecularDynamics(topology_file="ioned_topol",input_structure="em",output_name="t_0",seed=1993,steps=100,pcoupling="semiisotropic",wallclock=24,epsilon=20,temperature=None,apolar=True,pme=False,umbrella_name=None):
if debug_status:
replace_steps(configuration['mdp_files'] + "cg-mdrun-50ns_sts.mdp","runfile.mdp")
elif pcoupling == "semiisotropic":
replace_seed(configuration['mdp_files'] + "cg-mdrun-50ns_sts.mdp","seeded.mdp",seed)
replace_epsilon("seeded.mdp","epsilon-correct.mdp",epsilon)
replace_temperature("epsilon-correct.mdp","retemp.mdp",temperature)
replace_steps("retemp.mdp","runfile.mdp",steps)
#replace_steps("seeded.mdp","runfile.mdp",steps)
elif pcoupling == "anisotropic":
replace_seed(configuration['mdp_files'] + "cg-mdrun-50ns_sts.mdp","seeded.mdp",seed)
replace_pcoupling("seeded.mdp","aniso_pcouple.mdp",coupling="anisotropic")
replace_epsilon("aniso_pcouple.mdp","epsilon-correct.mdp",epsilon)
replace_temperature("epsilon-correct.mdp","retemp.mdp",temperature)
replace_steps("retemp.mdp","runfile.mdp",steps)
#replace_steps("aniso_pcouple.mdp","runfile.mdp",steps)
#replace_steps("epsilon-correct.mdp","runfile.mdp",steps)
else:
print "Error- pcoupling type not recognised"
sys.exit()
if not apolar:
print "Polar martini parameters in use: changing the appropriate parameters"
pmartini_update("runfile.mdp")
#This is a special change- so that all CG systems can have a common wallclock we specifically increase it for PMARTINI
wallclock *= 4
if pme:
print "Turning on PME. Unknown effects. Here be dragons"
pme_update("runfile.mdp")
#This is a special change- so that all CG systems can have a common wallclock we specifically increase it for PMARTINI
wallclock *= 4
#os.system(gromacs+"grompp -f runfile -c " + input_structure + " -p " + topology_file + " -o " + output_name + " >& grompp_" + output_name + ".log")
#os.system(gromacs+"mdrun -deffnm " + output_name)
UserDefSimulation(topology_file,input_structure,output_name,"runfile",wallclock=wallclock,wallclock_lifetime=wallclock,umbrella=umbrella_name)
default_timestep = 0.02
reducer=1
reduce_values = ("dt")
increase_values = ("nstxout","nstvout","nstlog","nstenergy","nstxtcout")
if output_name + ".gro" not in os.listdir("."):
reducer *= 0.5
#if reducer >= 0.25:
timestep = reducer * default_timestep
restart_name = "restart_" + str(timestep)
#Determine last frame
logfile = open(output_name+".log")
logcontents = logfile.readlines()
for i in range(len(logcontents)):
line = logcontents[i]
contents = line.split()
if len(contents) == 3:
if contents[0] == "Step":
if len (logcontents[i+1].split()) == 3:
lasttime = float(logcontents[i+1].split()[1])
logfile.close()
#final time is the final 2-thousandth frame
finaltime = int(lasttime/2000)*2000
if finaltime < 0: finaltime = 0
os.system("echo '0\n' | " + gromacs + "trjconv -s " + output_name + ".tpr -f " + output_name + ".trr -dump " + str(finaltime) + " -o " + restart_name + "_ini.gro")
#read the runfile and write out updated lines (with smaller timestep etc) to restart.mdp
restart_mdp = open(restart_name + ".mdp","w")
old_mdp = open("runfile.mdp","r")
for line in old_mdp:
contents = line.split()
if len(contents) == 0 or len(contents) == 1:
print >> restart_mdp, line
elif contents[0] in reduce_values:
for_restart = contents[0] + " = " + str(float(contents[2]) * reducer)
print >> restart_mdp, for_restart
elif contents[0] in increase_values:
for_restart = contents[0] + " = " + str(float(contents[2]) / reducer)
print >> restart_mdp, for_restart
elif contents[0] == "tinit":
print >> restart_mdp, "tinit = " + str(finaltime)
elif contents[0] == "nsteps":
#The number of steps should be the new total number of steps minus the number that would have been done
previous_steps = float(finaltime)/timestep
new_total_steps = steps / reducer - previous_steps
print >> restart_mdp, "nsteps = " + str(new_total_steps)
elif contents[0] == "gen_vel":
print >> restart_mdp, "gen_vel = no"
else:
print >> restart_mdp, line
restart_mdp.close()
old_mdp.close()
#Run
UserDefSimulation(topology_file,restart_name+"_ini.gro",restart_name,restart_name+".mdp",umbrella=umbrella_name)
#Remove broken frames from the trajectory, after the time point
os.system(gromacs + "trjconv -f " + output_name + ".xtc -e "+ str(finaltime) + " -o " + output_name + ".xtc")
#concatenated output_name.xtc and restart.xtc to output_name.xtc
os.system(gromacs + "trjcat -f " + output_name + ".xtc " + restart_name + ".xtc -o " + output_name + ".xtc")
#move restart.gro to output_name.gro
os.rename(restart_name + ".gro", output_name + ".gro")
charge_flag = "-np"
charge = -int(charge)
ion_name = "NA+"
os.system("echo '13\n' | " + gromacs+"genion -s solvated.tpr -o ioned.pdb " + charge_flag + " " + str(charge))
ion_topology.write("DPPC " + str(lipids) + "\nW " + str(water-charge) + "\n")
ion_topology.write(ion_name + " "*7 + str(charge))
ion_topology.flush()
ion_topology.close()
os.system(gromacs+"grompp -f " + configuration['mdp_files'] + "cg-em_extended -c ioned.pdb -p ioned_topol -o em >& grompp_em.log")
os.system(gromacs+"mdrun -deffnm em")
if debug_status:
replace_steps(configuration['mdp_files'] + "cg-mdrun-50ns_sts.mdp","runfile.mdp")
else:
replace_seed(configuration['mdp_files'] + "cg-mdrun-50ns_sts.mdp","seeded.mdp",seed)
replace_steps("seeded.mdp","runfile.mdp",10000000)
os.system(gromacs+"grompp -f runfile -c em -p ioned_topol -o t_0 >& grompp_md.log")
os.system(gromacs+"mdrun -deffnm t_0")
#analyse
length = len(initial_sequence)
if length %2 == 0:
middle_residues = str(length/2 - 1) + "-" + str(length/2 +2)
else:
middle_residues = str(length/2 - 1) + "-" + str(length/2 +1)
if charge != 0:
str(charge))
ion_topology.write("DPPC " + str(lipids) + "\nW " +
str(water - charge) + "\n")
ion_topology.write(ion_name + " " * 7 + str(charge))
ion_topology.flush()
ion_topology.close()
os.system(gromacs + "grompp -f " + configuration['mdp_files'] +
"cg-em_extended -c ioned.pdb -p ioned_topol -o em >& grompp_em.log")
os.system(gromacs + "mdrun -deffnm em")
if debug_status:
replace_steps(configuration['mdp_files'] + "cg-mdrun-50ns_sts.mdp",
"runfile.mdp")
else:
replace_seed(configuration['mdp_files'] + "cg-mdrun-50ns_sts.mdp",
"seeded.mdp", seed)
replace_steps("seeded.mdp", "runfile.mdp", 10000000)
os.system(gromacs +
"grompp -f runfile -c em -p ioned_topol -o t_0 >& grompp_md.log")
os.system(gromacs + "mdrun -deffnm t_0")
#analyse
length = len(initial_sequence)
if length % 2 == 0:
middle_residues = str(length / 2 - 1) + "-" + str(length / 2 + 2)
else:
middle_residues = str(length / 2 - 1) + "-" + str(length / 2 + 1)
def RobustMolecularDynamics(topology_file="ioned_topol",
input_structure="em",
output_name="t_0",
seed=1993,
steps=100,
pcoupling="semiisotropic",
wallclock=24,
epsilon=20,
temperature=None,
apolar=True,
pme=False,
umbrella_name=None):
if debug_status:
replace_steps(configuration['mdp_files'] + "cg-mdrun-50ns_sts.mdp",
"runfile.mdp")
elif pcoupling == "semiisotropic":
replace_seed(configuration['mdp_files'] + "cg-mdrun-50ns_sts.mdp",
"seeded.mdp", seed)
replace_epsilon("seeded.mdp", "epsilon-correct.mdp", epsilon)
replace_temperature("epsilon-correct.mdp", "retemp.mdp", temperature)
replace_steps("retemp.mdp", "runfile.mdp", steps)
#replace_steps("seeded.mdp","runfile.mdp",steps)
elif pcoupling == "anisotropic":
replace_seed(configuration['mdp_files'] + "cg-mdrun-50ns_sts.mdp",
"seeded.mdp", seed)
replace_pcoupling("seeded.mdp",
"aniso_pcouple.mdp",
coupling="anisotropic")
replace_epsilon("aniso_pcouple.mdp", "epsilon-correct.mdp", epsilon)
replace_temperature("epsilon-correct.mdp", "retemp.mdp", temperature)
replace_steps("retemp.mdp", "runfile.mdp", steps)
#replace_steps("aniso_pcouple.mdp","runfile.mdp",steps)
#replace_steps("epsilon-correct.mdp","runfile.mdp",steps)
else:
print "Error- pcoupling type not recognised"
sys.exit()
if not apolar:
print "Polar martini parameters in use: changing the appropriate parameters"
pmartini_update("runfile.mdp")
#This is a special change- so that all CG systems can have a common wallclock we specifically increase it for PMARTINI
wallclock *= 4
if pme:
print "Turning on PME. Unknown effects. Here be dragons"
pme_update("runfile.mdp")
#This is a special change- so that all CG systems can have a common wallclock we specifically increase it for PMARTINI
wallclock *= 4
#os.system(gromacs+"grompp -f runfile -c " + input_structure + " -p " + topology_file + " -o " + output_name + " >& grompp_" + output_name + ".log")
#os.system(gromacs+"mdrun -deffnm " + output_name)
UserDefSimulation(topology_file,
input_structure,
output_name,
"runfile",
wallclock=wallclock,
wallclock_lifetime=wallclock,
umbrella=umbrella_name)
default_timestep = 0.02
reducer = 1
reduce_values = ("dt")
increase_values = ("nstxout", "nstvout", "nstlog", "nstenergy",
"nstxtcout")
if output_name + ".gro" not in os.listdir("."):
reducer *= 0.5
#if reducer >= 0.25:
timestep = reducer * default_timestep
restart_name = "restart_" + str(timestep)
#Determine last frame
logfile = open(output_name + ".log")
logcontents = logfile.readlines()
for i in range(len(logcontents)):
line = logcontents[i]
contents = line.split()
if len(contents) == 3:
if contents[0] == "Step":
if len(logcontents[i + 1].split()) == 3:
lasttime = float(logcontents[i + 1].split()[1])
logfile.close()
#final time is the final 2-thousandth frame
finaltime = int(lasttime / 2000) * 2000
if finaltime < 0: finaltime = 0
os.system("echo '0\n' | " + gromacs + "trjconv -s " + output_name +
".tpr -f " + output_name + ".trr -dump " + str(finaltime) +
" -o " + restart_name + "_ini.gro")
#read the runfile and write out updated lines (with smaller timestep etc) to restart.mdp
restart_mdp = open(restart_name + ".mdp", "w")
old_mdp = open("runfile.mdp", "r")
for line in old_mdp:
contents = line.split()
if len(contents) == 0 or len(contents) == 1:
print >> restart_mdp, line
elif contents[0] in reduce_values:
for_restart = contents[0] + " = " + str(
float(contents[2]) * reducer)
print >> restart_mdp, for_restart
elif contents[0] in increase_values:
for_restart = contents[0] + " = " + str(
float(contents[2]) / reducer)
print >> restart_mdp, for_restart
elif contents[0] == "tinit":
print >> restart_mdp, "tinit = " + str(
finaltime)
elif contents[0] == "nsteps":
#The number of steps should be the new total number of steps minus the number that would have been done
previous_steps = float(finaltime) / timestep
new_total_steps = steps / reducer - previous_steps
print >> restart_mdp, "nsteps = " + str(
new_total_steps)
elif contents[0] == "gen_vel":
print >> restart_mdp, "gen_vel = no"
else:
print >> restart_mdp, line
restart_mdp.close()
old_mdp.close()
#Run
UserDefSimulation(topology_file,
restart_name + "_ini.gro",
restart_name,
restart_name + ".mdp",
umbrella=umbrella_name)
#Remove broken frames from the trajectory, after the time point
os.system(gromacs + "trjconv -f " + output_name + ".xtc -e " +
str(finaltime) + " -o " + output_name + ".xtc")
#concatenated output_name.xtc and restart.xtc to output_name.xtc
os.system(gromacs + "trjcat -f " + output_name + ".xtc " +
restart_name + ".xtc -o " + output_name + ".xtc")
#move restart.gro to output_name.gro
os.rename(restart_name + ".gro", output_name + ".gro")