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PolymerChain.py
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import numpy as np
from openmm.app import *
from openmm import *
import openmm.unit as unit
from sys import stdout
from itertools import product
import os
import topo
import misc
import simulation_details as sd
class PolymerChain:
def __init__(self, id, monomers, n_of_monomers, toppar, charmm="charmm"):
self.charmm = charmm
self.id = id
self.monomers = monomers
self.n_of_monomers = n_of_monomers
self.backbone_atoms = []
self.patches = []
self.totmon = len(self.monomers)
self.chain_length = np.sum(n_of_monomers)
# generate the monomer geometries
header = "RESI"
residues = []
current_atoms = []
self.toppar = toppar
# done =[]
with open(toppar, "r") as t:
for line in t:
# line= line.split('!')[0]
if line.startswith("!"):
continue
if line.startswith(header) and current_atoms:
residues.append(current_atoms[:])
current_atoms = []
if line.startswith("END"):
residues.append(current_atoms[:])
break
# print(line)
current_atoms.append(line)
for i in residues:
for j in i:
if j == "\n" or j.startswith("!"):
i.remove(j)
self.masses = topo.mass(residues[0])
residues_in_chain = []
for i in self.monomers:
for k in residues:
if k[0].split()[1] == i:
residues_in_chain.append(k)
bonds = []
angles = []
dihedrals = []
nonb = []
section = None
for line in t:
if line.startswith("END"):
break
if (
line.startswith("!")
or line.startswith("\n")
or line.startswith(" ")
):
continue
elif line.startswith("BOND"):
section = "BOND"
continue
elif line.startswith("ANGL"):
section = "ANGLE"
continue
elif line.startswith("DIHE"):
section = "DIHE"
continue
elif line.startswith("NONB"):
section = "NONB"
continue
elif line.startswith("NBFIX"):
section = "NBFIX"
continue
line = line.split("!")[0]
if section == "BOND":
bonds.append(line)
if section == "ANGLE":
angles.append(line)
if section == "DIHE":
dihedrals.append(line)
if section == "NONB":
nonb.append(line)
self.residues = []
self.angles = []
self.bonds = []
self.dihedrals = []
self.nonb = []
for i in angles:
# print(i.split())
self.angles.append(topo.Angle_type(*i.split()))
for i in bonds:
self.bonds.append(topo.Bond_type(*i.split()))
for i in dihedrals:
# print(i)
self.dihedrals.append(topo.Dihedral_type(*i.split()))
for i in nonb[1:]:
# print(i)
self.nonb.append(topo.Nonb(*i.split()))
for k in residues_in_chain:
# try:
self.residues.append(topo.Residue(k))
# except:
# print(k)
# quit()
##all residues in toppar submitted
self._allresidues = []
for l in residues[1:]:
self._allresidues.append(topo.Residue(l))
def build_Monomers(self, verbose=False):
# Building Monomer psf/crd using internal coordinates
for k in self.residues:
if len(k.atoms) >= 3:
f = open("tmp.inp", "w")
f.write(f"ioformat extended \nstream {self.toppar}\n\n")
f.write(f"read sequence {k.name} 1 \n")
f.write(f"generate {k.name} first none last none\n")
f.write("\nic gene\nic param\n")
f.write(
f"ic seed {k.name} 1 {k.atoms[2].name} {k.name} 1 {k.atoms[1].name} {k.name} 1 {k.atoms[0].name}\n"
)
f.write("ic build\ncoor shake\nenergy\nmini sd nstep 600\n")
f.write(f"write coor card name {k.name}.crd\n")
f.write(f"write psf card xplor name {k.name}.psf\n")
f.write("stop")
f.close()
os.system(f"{self.charmm} -i tmp.inp >tmp.out")
if not verbose:
os.system("rm tmp.inp")
os.system("rm tmp.out")
else:
print(f"{k.name} not enough atoms for ic")
continue
def build_simpleChain(
self, dyna=False, dynastep=500, verbose=False, random=False, iter=3
):
print(
f"BUILDing Chain\nTEA_PUN powered by CHARMM\nmake sure you have the correct patches and residues in the toppar before running this step!\nIC blocks may be needed for complex monomers"
)
names = []
segid = []
segid_num = []
seg_atoms = []
atoms = []
ids = []
f = open("tmp.inp", "w")
f.write(
f"dimension chsize 450000\nioformat extended \nstream {self.toppar}\n\n"
)
##################################################################################################################################################
##combining the blocks for reading them into charmm###############################################################################################
##################################################################################################################################################
for k in range(len(self.residues)):
if self.residues[k].name not in segid:
segid.append(self.residues[k].name)
seg_atoms.append(self.residues[k].atoms)
segid_num.append(self.n_of_monomers[k])
else:
segid_num[
segid.index(self.residues[k].name)
] += self.n_of_monomers[k]
for segment in range(len(segid)):
f.write(f"read sequence {segid[segment]} {segid_num[segment]}\n")
f.write(f"\ngenerate {segid[segment]} first none last none\n")
#################################################################################################################################################
##here the atoms are assigned to correct residues for IC seed####################################################################################
#################################################################################################################################################
for res in range(len(self.residues)):
for i in range(self.n_of_monomers[res]):
names.append(self.residues[res].name)
atoms.append(self.residues[res].atoms)
f.write("AUTOGENerate OFF\n")
f.write("ic gene\n")
ctr = 1
#################################################################################################################################################
# parameters for displaceing monomers#############################################################################################################
#################################################################################################################################################
z_vector = 0.4
r = (z_vector * self.chain_length) / 2
f.write("bomblev -5\n")
for m in range(len(names)):
c = names[:m].count(names[m])
ids.append(c + 1)
####################################################
##Random Walk
####################################################
coords = misc.randomwalk(self.chain_length, 4)
if random:
import random
c = list(zip(names, atoms, ids))
random.shuffle(c)
names, atoms, ids = zip(*c)
######################################################
# writing the charmm input
######################################################
for num in range(len(names)):
n = names[num]
try:
f.write(
f"ic param\nic seed {n} {ids[num]} {atoms[num][1].name} {n} {ids[num]} {atoms[num][0].name} {n} {ids[num]} {atoms[num][3].name}\n"
)
except:
f.write(
f"coor set sele (segid {n} .and. resid {ids[num]}) end xdir 0 ydir 0 zdir 0\n"
)
f.write(
f"coor trans sele (segid {n} .and. resid {ids[num]}) end xdir {coords[num][0]} ydir {coords[num][1]} zdir {coords[num][2]}\n"
) # add function to find real bondlenght
if ctr > 1 and ctr <= self.chain_length:
f.write(
f"patch {misc.find_patch(prev_seg,n)} {prev_seg} {prev} {n} {ids[num]}\n"
)
prev = ids[num]
ctr += 1
prev_seg = n
f.write("ic build\n")
f.write(f"rename segid {self.id} sele all end\ncoor shake\n")
f.write("autogen angl dihe \n")
f.write("bomblev -5\n")
f.write("energy\n")
for i in range(iter):
f.write(f"mini sd nstep 10000\n")
f.write(f"write coor card name {self.id.lower()}.crd\n")
f.write("mini abnr nstep 300\n")
if dyna:
f.write(f"DYNA nstep {dynastep}\n")
f.write(f"write psf card xplor name {self.id.lower()}.psf\n")
f.write(f"write coor card name {self.id.lower()}.crd\n")
f.write("stop")
f.close()
print("invoking charmm-process")
os.system(f"{self.charmm} -i tmp.inp >build.out")
if verbose == False:
os.system("rm tmp.inp")
os.system("rm build.out")
def relax_chain(self, nstep=150_000, useBMH=False):
#####################################################################################################################################################
# Compressing the chain in a Force Cage and relaxing afterwards to get usable starting structures for MD
#####################################################################################################################################################
# setting up openMM
print(
f"RELAxing Chain\nTEA_PUN powered by openMM\nmake sure you have a psf and crd before running this step!(example:chainID.psf/chainID.crd)"
)
psf = CharmmPsfFile(f"{self.id.lower()}.psf")
crd = CharmmCrdFile(f"{self.id.lower()}.crd")
toppar = CharmmParameterSet(f"{self.toppar}")
DEFAULT_PLATFORMS = "CUDA", "OpenCL", "CPU"
enabled_platforms = [
Platform.getPlatform(i).getName()
for i in range(Platform.getNumPlatforms())
]
for platform in DEFAULT_PLATFORMS:
if platform in enabled_platforms:
platform = Platform.getPlatformByName(platform)
break
print("Using platform:", platform.getName())
prop = (
dict(CudaPrecision="mixed")
if platform.getName() == "CUDA"
else dict()
)
print("BUILDing SYSTem")
#######################################################################################
psf = misc.gen_box(psf, crd, enforce_cubic=True)
########################################################################################################################################################
system = psf.createSystem(
toppar,
nonbondedMethod=CutoffNonPeriodic,
nonbondedCutoff=1.5 * unit.nanometer,
solventDielectric=60,
constraints=None,
)
# #########################################################################################################################################################
# Initialize Simulation
################################################################################################
integrator = NoseHooverIntegrator(
300 * unit.kelvin, 50 / unit.picosecond, 0.0001 * unit.picoseconds
)
# system, epsilons, sigm = eliminate_LJ(psf)
# system = usemodBMH(self, psf, epsilons, sigm, NBfix=False)
simulation = Simulation(
psf.topology, system, integrator, platform, prop
)
simulation.context.setPositions(crd.positions)
simulation.reporters.append(
StateDataReporter(
stdout,
1_000,
step=True,
time=True,
totalEnergy=True,
speed=True,
separator="\t",
)
)
if useBMH:
system, epsilons, sigm = sd.eliminate_LJ(psf)
# print(np.sum(epsilons))
# system = eliminate_elec(psf)
system = sd.usemodBMH(self, psf, epsilons, sigm, NBfix=True)
# system.addForce(MonteCarloBarostat(1 * unit.atmospheres, 300 * unit.kelvin, 10))
simulation.context.setVelocitiesToTemperature(300 * unit.kelvin)
###############################################################################################
# Compress System
###############################################################################################
print("MINImizing ENERgy")
simulation.minimizeEnergy(maxIterations=1_500)
print("\nINITial SYSTem ENERgy")
print(simulation.context.getState(getEnergy=True).getPotentialEnergy())
simulation.reporters.append(
DCDReporter(f"{self.id.lower()}_relax.dcd", int(nstep / 100))
)
simulation.reporters.append(
PDBReporter(f"{self.id.lower()}_relax.pdb", nstep)
)
print("STARting DYNAmics")
simulation.step(10_000)
integrator.setStepSize(0.002 * unit.picoseconds)
simulation.step(10_000)
integrator.setStepSize(0.003 * unit.picoseconds)
simulation.context.reinitialize(preserveState=True)
simulation.step(nstep)
state = simulation.context.getState(
getPositions=True, getVelocities=True
)
with open(f"{self.id.lower()}_relax.rst", "w") as f:
f.write(XmlSerializer.serialize(state))
def solvate_charmm(
self,
num_of_Polymers,
solvent_res,
solvent_num,
pack=False,
build=True,
verbose=False,
pdb_file="default",
solvent_pdb="default",
crd="default",
boxsize=1500,
salt=False,
c="",
c_pdb="",
c_n=0,
a="",
a_pdb="",
a_n=0,
square=False,
read=False,
n_proc=16,
):
######################################################################################################
##Set pdbfile for packing to default if not defined
######################################################################################################
if pdb_file == "default":
pdb_file = f"{self.id.lower()}_relax.pdb"
if crd == "default":
crd = f"{self.id.lower()}.crd"
######################################################################################################
# checking toppar for Solvent residue
######################################################################################################
found = False
for i in self._allresidues:
try:
if solvent_res == i.name:
print("Solvent found in toppar")
atoms = i.atoms
found = True
break
except AttributeError:
pass
if salt:
for i in self._allresidues:
try:
if c == i.name:
print("cation found in toppar")
found = True
break
except AttributeError:
pass
for i in self._allresidues:
try:
if a == i.name:
print("anion found in toppar")
found = True
break
except AttributeError:
pass
spacing = 5
if square:
x = np.linspace(0, int(boxsize), int(boxsize // spacing))
y = np.linspace(0, int(boxsize), int(boxsize // spacing))
z = np.linspace(0, int(boxsize), int(boxsize // spacing))
else:
x = np.linspace(0, int(boxsize), int(boxsize // spacing))
y = np.linspace(
0, int(boxsize * 0.9), int(boxsize * 0.9 // spacing)
)
z = np.linspace(
0, int(boxsize * 0.8), int(boxsize * 0.8 // spacing)
)
coords = product(x, y, z)
if build:
solvent = misc.solvation_coordinates(x, y, z, solvent_res, atoms)
elif read:
solvent = "slvnt.crd"
if solvent_num == "auto":
solvent_num = len(list(coords))
coords = product(x, y, z)
if not found:
print(f"ERRor something not in toppar!")
return
#######################################################################################################
#######################################################################################################
print("GENErating PSF\nTEA_PUN powered by CHARMM\n")
#######################################################################################################
f = open("tmp.inp", "w")
f.write(
f"dimension chsize 50000000\nioformat extended\nstream {self.toppar}\nset parall {n_proc}\n"
)
f.write(f"open unit 1 card name {self.id.lower()}.psf\n")
f.write(f"read psf card unit 1 \n")
f.write("close unit 1\n")
if build or read:
f.write(f"open unit 2 card name {crd}\n") #
f.write(f"read coor card unit 2 \n")
f.write("close unit 2\n")
f.write(
f"coor trans sele segid {self.id} end xdir {boxsize/2} ydir {boxsize/2} zdir {boxsize/2}\n"
)
if num_of_Polymers != 1:
f.write(
f"coor trans sele segid {self.id} end xdir -50 ydir 0 zdir 0\n"
)
f.write(f"rename segid {self.id}_1 sele all end\n")
f.write(f"")
for i in range(num_of_Polymers - 1):
f.write(f"generate {self.id}_{i+2} duplicate {self.id}_1\n")
f.write(
f"coor dupl sele segid {self.id}_{i+1} end sele segid {self.id}_{i+2} end\n"
)
f.write(
f"coor trans sele segid {self.id}_{i+2} end xdir 50 ydir 0 zdir 0\n"
)
f.write(
f"read sequence {solvent_res} {solvent_num}\ngenerate {solvent_res} first none last none noangle nodihedral setup warn\n"
)
if build or read:
f.write(f"open unit 15 card name {solvent}\n") #
f.write(f"read coor append card unit 15 \n")
f.write(
f"bomblev -1\ndelete atom sele .byres. (segid {solvent_res} .and. segid {self.id} .around. 5.5) end\n"
)
if num_of_Polymers != 1:
for i in range(num_of_Polymers):
f.write(
f"bomblev -1\ndelete atom sele .byres. (segid {solvent_res} .and. segid {self.id}_{i+1} .around. 5.5) end\n"
)
if salt:
f.write(
f"read sequence {c} {c_n}\ngenerate {c} first none last none setup warn\n"
)
f.write(
f"read sequence {a} {a_n}\ngenerate {a} first none last none setup warn\n"
)
# f.write("\nenergy\nmini sd nstep 500\n")
f.write(
f"open unit 10 write form name ./{self.id.lower()}_in_{solvent_res.lower()}.psf\nwrite unit 10 psf xplor card\nclose unit 10\n"
)
f.write(
f"write coor card name {self.id.lower()}_in_{solvent_res.lower()}.crd\n\nstop"
)
f.close()
print("invoking charmm-process")
os.system(f"{self.charmm} -i tmp.inp >solvate.out")
print(f"check {self.id.lower()}_in_{solvent_res.lower()}.psf")
#######################################################################################################
#######################################################################################################
if verbose == False:
os.system("rm tmp.inp")
os.system("rm solvate.out")
os.system("rm slvnt.crd")
#######################################################################################################
# refering to packmol!
#######################################################################################################
if pack:
if solvent_pdb == "default":
solvent_pdb = f"{solvent_res.lower()}.pdb"
misc.pack_system(
pdb_file,
num_of_Polymers,
solvent_res,
solvent_pdb,
solvent_num,
verbose=verbose,
boxsize=boxsize,
salt=salt,
cat=c_pdb,
c_n=c_n,
an=a_pdb,
a_n=a_n,
)
def solvate(
self,
num_of_Polymers,
solvent_res,
solvent_num,
build=True,
verbose=False,
pdb_file="default",
usepdb=False,
crd="default",
boxsize=1500,
salt=False,
c="",
c_pdb="",
c_n=0,
a="",
a_pdb="",
a_n=0,
square=False,
read=False,
n_proc=16,
mini=False,
iter=1,
chsize=50000000,
spacing=5,
):
######################################################################################################
##Set pdbfile for packing to default if not defined
######################################################################################################
if pdb_file == "default":
pdb_file = f"{self.id.lower()}_relax.pdb"
if crd == "default":
crd = f"{self.id.lower()}.crd"
######################################################################################################
# checking toppar for Solvent residue
######################################################################################################
found = False
for i in self._allresidues:
try:
if solvent_res == i.name:
print("Solvent found in toppar")
atoms = i.atoms
found = True
break
except AttributeError:
pass
if salt:
for i in self._allresidues:
try:
if c == i.name:
print("cation found in toppar")
found = True
break
except AttributeError:
pass
for i in self._allresidues:
try:
if a == i.name:
print("anion found in toppar")
found = True
break
except AttributeError:
pass
if not found:
print(f"ERRor something not in toppar!")
return
if square:
x = np.linspace(0, int(boxsize), int(boxsize // spacing))
y = np.linspace(0, int(boxsize), int(boxsize // spacing))
z = np.linspace(0, int(boxsize), int(boxsize // spacing))
else:
x = np.linspace(0, int(boxsize), int(boxsize // spacing))
y = np.linspace(
0, int(boxsize * 0.9), int(boxsize * 0.9 // spacing)
)
z = np.linspace(
0, int(boxsize * 0.8), int(boxsize * 0.8 // spacing)
)
coords = product(x, y, z)
if build:
solvent = misc.solvation_coordinates(x, y, z, solvent_res, atoms)
elif read:
solvent = "slvnt.crd"
if solvent_num == "auto":
solvent_num = len(list(coords))
coords = product(x, y, z)
#######################################################################################################
#######################################################################################################
print("GENErating PSF\nTEA_PUN powered by CHARMM\n")
#######################################################################################################
f = open("tmp.inp", "w")
f.write(
f"dimension chsize {int(chsize)} \nioformat extended\nstream {self.toppar}\nset parall {n_proc}\n"
)
f.write(f"open unit 1 card name {self.id.lower()}.psf\n")
f.write(f"read psf card unit 1 \n")
f.write("close unit 1\n")
if usepdb:
f.write(f"bomblev -1\n") #
f.write(f"open unit 2 form read name {pdb_file}\n") #
f.write(f"read coor pdb unit 2 \n")
f.write("close unit 2\n")
elif not usepdb:
f.write(f"open unit 2 card name {crd}\n") #
f.write(f"read coor card unit 2 \n")
f.write("close unit 2\n")
f.write(f"coor stat sele all end \n")
if square:
f.write(
f"calc x = {boxsize/2}-?XAVE\ncalc y = {boxsize/2}-?YAVE\ncalc z = {boxsize/2}-?ZAVE"
)
else:
f.write(
f"calc x = {boxsize/2}-?XAVE\ncalc y = {(boxsize*.9)/2}-?YAVE\ncalc z = {(boxsize*.8)/2}-?ZAVE\n"
)
f.write(
f"\ncoor trans xdir @x\ncoor trans ydir @y \ncoor trans zdir @z\n"
)
if num_of_Polymers != 1:
f.write(
f"coor trans sele segid {self.id} end xdir -100 ydir 0 zdir 0\n"
)
f.write(f"rename segid {self.id}_1 sele all end\n")
f.write(f"\n")
for i in range(num_of_Polymers - 1):
f.write(f"generate {self.id}_{i+2} duplicate {self.id}_1\n")
f.write(
f"coor dupl sele segid {self.id}_{i+1} end sele segid {self.id}_{i+2} end\n"
)
f.write(
f"coor trans sele segid {self.id}_{i+2} end xdir 250 ydir 0 zdir 0\n"
)
f.write(f"write coor card name {self.id.lower()}_n.crd\n")
f.write(
f"read sequence {solvent_res} 1\ngenerate {solvent_res} first none last none noangle nodihedral setup warn\n"
)
f.write(
f"open unit 10 write form name ./{self.id.lower()}_in_{solvent_res.lower()}.psf\nwrite unit 10 psf xplor card\nclose unit 10\n"
)
f.write(
f"write coor card name {self.id.lower()}_in_{solvent_res.lower()}.crd\n\nstop"
)
f.close()
print("invoking charmm-process")
os.system(f"{self.charmm} -i tmp.inp >solvate.out")
print("Switching to Parmed")
misc.make_psf(
f"{self.id.lower()}_in_{solvent_res.lower()}.psf", solvent_num
)
print("invoking charmm-process")
f = open("tmp.inp", "w")
f.write(
f"dimension chsize {int(chsize)} \nioformat extended\nstream {self.toppar}\nset parall {n_proc}\n"
)
f.write(
f"open unit 1 card name {self.id.lower()}_in_{solvent_res.lower()}.psf\n"
)
f.write(f"read psf card unit 1 \n")
f.write("close unit 1\n")
f.write(f"open unit 2 card name {self.id.lower()}_n.crd\n") #
f.write(f"read coor card unit 2 \n")
f.write("close unit 2\n")
f.write(f"open unit 15 card name {solvent}\n") #
f.write(f"read coor append card unit 15 \n")
f.write(
f"bomblev -1\ndelete atom sele .byres. (segid {solvent_res} .and. segid {self.id} .around. 5.5) end\n"
)
if num_of_Polymers != 1:
for i in range(num_of_Polymers):
f.write(
f"bomblev -1\ndelete atom sele .byres. (segid {solvent_res} .and. segid {self.id}_{i+1} .around. 5.5) end\n"
)
if mini:
# f.write("\nbomblev -4\n")
for i in range(iter):
f.write("\nenergy\nmini sd nstep 500\n")
f.write(
f"open unit 10 write form name ./{self.id.lower()}_in_{solvent_res.lower()}.psf\nwrite unit 10 psf xplor card\nclose unit 10\n"
)
f.write(
f"write coor card name {self.id.lower()}_in_{solvent_res.lower()}.crd\n\nstop"
)
f.close()
os.system(f"{self.charmm} -i tmp.inp >solvate_2.out")
print(f"check {self.id.lower()}_in_{solvent_res.lower()}.psf")
#######################################################################################################
#######################################################################################################
if verbose == False:
os.system("rm tmp.inp")
os.system("rm solvate.out")
os.system("rm solvate_2.out")
os.system("rm slvnt.crd")
def equilibrate(
self,
psf,
pdb,
nstep=2_000_000,
iter=50,
dt=0.0001,
p=10,
T=300,
useBMH=False,
freeze=False,
multiplicator=1.1,
octahedron=False,
mini=True,
):
print(f"EQUIlibrate Chain\nTEA_PUN powered by openMM")
psf = CharmmPsfFile(psf)
try:
pdb = PDBFile(pdb)
except:
pdb = CharmmCrdFile(pdb)
params = CharmmParameterSet(self.toppar)
DEFAULT_PLATFORMS = "CUDA", "OpenCL", "CPU"
enabled_platforms = [
Platform.getPlatform(i).getName()
for i in range(Platform.getNumPlatforms())
]
for platform in DEFAULT_PLATFORMS:
if platform in enabled_platforms:
platform = Platform.getPlatformByName(platform)
break
print(f"Using {platform.getName()}")
prop = (
dict(CudaPrecision="mixed")
if platform.getName() == "CUDA"
else dict()
)
psf = misc.gen_box(psf, pdb)
system = psf.createSystem(
params,
nonbondedMethod=CutoffPeriodic,
nonbondedCutoff=1.5 * unit.nanometer,
constraints=None,
)
integrator = NoseHooverIntegrator(
5 * unit.kelvin, 50 / unit.picosecond, 0.00005 * unit.picoseconds
)
if useBMH:
system, epsilons, sigm = sd.eliminate_LJ(psf)
# print(np.sum(epsilons))
system = sd.usemodBMH(
PolymerChain=self,
psf=psf,
epsilons=epsilons,
sigm=sigm,
NBfix=True,
)
if freeze:
system = sd.freeze_polymer(psf, self)
simulation = Simulation(
psf.topology, system, integrator, platform, prop
)
simulation.context.setPositions(pdb.positions)
if octahedron:
try:
boxVectors = sd.set_octahedron(psf, multiplicator)
print(f"setting {boxVectors}")
simulation.context.setPeriodicBoxVectors(*boxVectors)
except:
print("failed to Transform into octahedron")
print("MINImizing ENERgy")
# except:
# print("ERRor while minimizing")
print(simulation.context.getState(getEnergy=True).getPotentialEnergy())
simulation.reporters.append(
StateDataReporter(
stdout,
2000,
step=True,
time=True,
potentialEnergy=True,
kineticEnergy=True,
totalEnergy=True,
temperature=True,
volume=True,
density=True,
speed=True,
separator="\t",
)
)
if mini:
integrator.setTemperature(5 * unit.kelvin)
integrator.setStepSize(0.000001 * unit.picoseconds)
simulation.context.reinitialize(preserveState=True)
simulation.context.setVelocitiesToTemperature(5 * unit.kelvin)
simulation.step(1_000)
simulation.minimizeEnergy(maxIterations=20_000)
simulation.reporters.append(DCDReporter(f"pre_comp.dcd", 10_000))
integrator.setTemperature(5 * unit.kelvin)
integrator.setStepSize(0.000001 * unit.picoseconds)
simulation.context.reinitialize(preserveState=True)
simulation.context.setVelocitiesToTemperature(5 * unit.kelvin)
simulation.step(500_000)
state = simulation.context.getState(
getPositions=True, getVelocities=True
)
with open("init.rst", "w") as f:
f.write(XmlSerializer.serialize(state))
# simulation.minimizeEnergy(maxIterations=200_000_000)
# simulation.minimizeEnergy(maxIterations=200_000)
# simulation.context.setVelocitiesToTemperature(5 * unit.kelvin)
# simulation.step(200_000)
# simulation.context.setVelocitiesToTemperature(5 * unit.kelvin)
# simulation.step(200_000)
# integrator.setStepSize(0.00005 * unit.picoseconds)
# simulation.context.reinitialize(preserveState=True)
# simulation.step(300_000)
# simulation.minimizeEnergy(maxIterations=2_000)
integrator.setTemperature(T * unit.kelvin)
integrator.setStepSize(dt * unit.picoseconds)
simulation.context.reinitialize(preserveState=True)
# simulation.minimizeEnergy(maxIterations=200_000_000)
simulation.step(200_000)
print("\nINITial SYSTem ENERgy")
print(simulation.context.getState(getEnergy=True).getPotentialEnergy())
pdbfile.PDBFile.writeModel(
simulation.topology,
simulation.context.getState(getPositions=True).getPositions(),
file=open("init.pdb", "w"),
)
ctr = 0
boxv = simulation.context.getState().getPeriodicBoxVectors()
# psf.boxVectors = boxv
for i in range(iter):
print(f"TimeStep set to {dt}ps")
state = simulation.context.getState(
getPositions=True, getVelocities=True
)
rst = f"{self.id.lower()}_temp.rst"
with open(rst, "w") as f:
f.write(XmlSerializer.serialize(state))
system = psf.createSystem(
params,
nonbondedMethod=CutoffPeriodic,
nonbondedCutoff=1.3 * unit.nanometer,
rigidWater=False,
solventDielectric=60,
)
integrator = NoseHooverIntegrator(
T * unit.kelvin, 50 / unit.picosecond, dt * unit.picoseconds
)
# barostat = system.addForce(
# MonteCarloBarostat(p * unit.atmospheres, 50 * unit.kelvin, 10)
# )
if useBMH:
system, epsilons, sigm = sd.eliminate_LJ(psf)
system = sd.usemodBMH(self, psf, epsilons, sigm, NBfix=True)
simulation = Simulation(
psf.topology, system, integrator, platform, prop
)
with open(rst, "r") as f:
simulation.context.setState(XmlSerializer.deserialize(f.read()))
simulation.reporters.append(
StateDataReporter(
stdout,
10_000,
step=True,
time=True,
potentialEnergy=True,
kineticEnergy=True,
totalEnergy=True,
temperature=True,
volume=True,
density=True,
speed=True,
separator="\t",
)
)
if ctr == 0:
try:
simulation.context.setPeriodicBoxVectors(*boxv)
print(
f"setting {simulation.context.getState().getPeriodicBoxVectors()}"
)
simulation.minimizeEnergy(maxIterations=2_000_000)
except:
print("failed\nusing init box")
if ctr > 0:
print(f"Using Dimensions: {boxv}")
simulation.context.setPeriodicBoxVectors(*boxv)
simulation.reporters.append(
DCDReporter(
f"{self.id.lower()}_equilibration_{dt}_{p}_{ctr}.dcd",
20_000,
)
)
# integrator.setTemperature(50 * unit.kelvin)
# simulation.context.reinitialize(preserveState=True)
# simulation.step(1000)
# system.removeForce(barostat)
# integrator.setTemperature(T * unit.kelvin)
# simulation.context.setVelocitiesToTemperature(T * unit.kelvin)
# simulation.context.reinitialize(preserveState=True)
simulation.step(500_000)
boxv = simulation.context.getState().getPeriodicBoxVectors()
state = simulation.context.getState(
getPositions=True, getVelocities=True
)
with open(rst, "w") as f:
f.write(XmlSerializer.serialize(state))
ctr += 1
system = psf.createSystem(
params,
nonbondedMethod=CutoffPeriodic,
nonbondedCutoff=1.5 * unit.nanometer,
constraints=None,
)
integrator = NoseHooverIntegrator(
300 * unit.kelvin, 50 / unit.picosecond, 0.004 * unit.picoseconds
)
if useBMH:
system, epsilons, sigm = sd.eliminate_LJ(psf)
print(np.sum(epsilons))
# system = eliminate_elec(psf)
system = sd.usemodBMH(self, psf, epsilons, sigm, NBfix=True)
simulation = Simulation(
psf.topology, system, integrator, platform, prop
)
with open(rst, "r") as f:
simulation.context.setState(XmlSerializer.deserialize(f.read()))
simulation.step(nstep)
self.boxv = simulation.context.getState().getPeriodicBoxVectors()
state = simulation.context.getState(
getPositions=True, getVelocities=True
)
with open(f"{self.id.lower()}.rst", "w") as f:
f.write(XmlSerializer.serialize(state))
def restart(
self,
psf,
rst,
nstep=2_000_000,
dt=0.0005,
p=10,
T=300,
iter=50,
useBMH=False,
freeze=False,
uPME=False,
pdb="init.pdb",
):
if uPME:
nb_meth = PME
else:
nb_meth = CutoffPeriodic
print(f"EQUIlibrate Chain\nTEA_PUN powered by openMM")
psf = CharmmPsfFile(psf)
# pdb = PDBFile("init.pdb")
params = CharmmParameterSet(self.toppar)
DEFAULT_PLATFORMS = "CUDA", "OpenCL", "CPU"
enabled_platforms = [
Platform.getPlatform(i).getName()
for i in range(Platform.getNumPlatforms())
]
for platform in DEFAULT_PLATFORMS:
if platform in enabled_platforms:
platform = Platform.getPlatformByName(platform)
break
print(f"Using {platform.getName()}")
prop = (
dict(CudaPrecision="mixed")
if platform.getName() == "CUDA"
else dict()
)
psf = misc.gen_box(
psf,
CharmmCrdFile("p1_in_bmw.crd"),