def Pickle(RepInd, Prefix):
''' pickles sim-style traj objects from each replica traj'''
# filenames
print 'Pickling Replica %d' % RepInd
TrajFile = Prefix + '.lammpstrj'
LogFile = Prefix + 'lammps.log'
myTrajFn = TrajFile + '.%d.gz' % RepInd
myLogFn = LogFile + '.%d' % RepInd
pickleTraj(myTrajFn, LogFile=myLogFn, LogFileToken='#run production')
return
def main(TrajFile, trajtype, fftype = 'wca', N_mon = 25, N_poly = 1, N_water = 1700, savedir = os.getcwd()):
Trj = pickleTraj(os.path.abspath(TrajFile))
# Computing
for measure in Measures:
if measure == 'pmf_Rg_R_EE' or isComputed(savedir, measure, trajtype): continue
print 'Computing %s for %s...' % (measure, trajtype)
data = compute(trj = Trj, trajtype = trajtype, measure = measure, nmon = N_mon, npoly = N_poly, nwater = N_water)
prefix = getFilePrefix(basedir = savedir, data_name = measure, data_type = 'measure', trajtype = trajtype)
writeToFile(prefix, data)
# Making histograms
for measure in Measures:
if isBinned(savedir, measure, trajtype): continue
print 'Binning %s...' % measure
hist_prefix = getFilePrefix(basedir = savedir, data_name = measure, data_type = 'hist', trajtype = trajtype)
if measure != 'pmf_Rg_R_EE':
compute_prefix = getFilePrefix(basedir = savedir, data_name = measure, data_type = 'measure', trajtype = trajtype)
data = readFromFile(compute_prefix)
hist = makeHist1D(data)
writeToFile(hist_prefix, hist)
if measure == 'pmf_Rg_R_EE':
Rg_prefix = getFilePrefix(basedir = savedir, data_name = 'Rg', data_type = 'measure', trajtype = trajtype)
R_EE_prefix = getFilePrefix(savedir, data_name = 'R_EE', data_type = 'measure', trajtype = trajtype)
Rg = readFromFile(Rg_prefix); R_EE = readFromFile(R_EE_prefix)
hist = makeHist2D(Rg, R_EE, fftype = fftype)
writeToFile(hist_prefix, hist)
def Update(self, TrajFn=None, Temp=None):
# updates the compute object if traj or temp is changed
# if native pdb is changed then better create another instance
if not Temp is None: self.Temp = Temp
if not TrajFn is None:
self.TrajFn = os.path.abspath(TrajFn)
self.Trj = pickleTraj(self.TrajFn)
self.FrameRange = range(0, len(self.Trj), StepFreq)
self.NFrames = len(self.FrameRange)
def parseTraj(lammpstraj): monomer_atomname = '3' Trj = pickleTraj(lammpstraj) boxlen = Trj.FrameData["BoxL"] mappedatoms = [] for (i, AtomName) in enumerate(Trj.AtomNames): if AtomName == monomer_atomname: mappedatoms.append(i) return (Trj, boxlen, mappedatoms)
def __prepHeadVars(): global Trj, BoxL, AtomNames, AtomTypes, NB, NW Trj = pickleTraj(Traj) BoxL = np.array(Trj.FrameData['BoxL']) AtomNames = Trj.AtomNames if AtomNames2Types: AtomTypes = __AtomName2Type(AtomNames) else: AtomTypes = Trj.AtomTypes if isMappedTrj: NB = len(np.where(AtomTypes == 1)[0]) NW = len(np.where(AtomTypes == 2)[0]) else: NB = len(np.where(AtomTypes < 13)[0]) NW = len(np.where(AtomTypes == 13)[0])
def __init_Srel(self, p, Sys, AATraj, cfg=None):
''' set Sys, Trj and Map for a single traj'''
self.NTraj = 1
self.p = p
self.cfg = cfg if not cfg is None else self.p.cfg
self.Sys = Sys
self.Allp = [self.p]
self.AllSys = [self.Sys]
self.AATraj = AATraj
# pickle supplied Traj
self.Trj = pickleTraj(self.AATraj)
# 1-1 map (since supplied traj will be already mapped)
Map = sim.atommap.PosMap()
for (i, a) in enumerate(self.Sys.Atom):
Map += [sim.atommap.AtomMap(Atoms1=i, Atom2=a)]
self.Map = Map
def __init__(self, NativePdb, TrajFn=None, Temp=None, Prefix='compute'):
# parse out-prefix
self.Prefix = os.path.abspath(Prefix)
self.OutPrefix = self.Prefix.split('/')[-1]
self.OutDir = os.path.dirname(self.Prefix)
# parse traj
if not TrajFn is None:
self.TrajFn = os.path.abspath(TrajFn)
self.Trj = pickleTraj(self.TrajFn)
self.FrameRange = range(0, len(self.Trj), StepFreq)
self.NFrames = len(self.FrameRange)
# record temp
if not Temp is None:
self.Temp = Temp
# cg protein objects for native and predicted
self.pNative = ProteinNCOS(NativePdb)
self.p = ProteinNCOS(NativePdb)
def makeSys(LDCut = 7.8, NMethane = 25, NWater = 1700):
print 'Making system'
atomtypeM = sim.chem.AtomType('M', Mass = 16.0427, Charge = 0.0)
atomtypeW = sim.chem.AtomType('W', Mass = 18.0, Charge = 0.0)
moltypeM = sim.chem.MolType('M', [atomtypeM])
moltypeW = sim.chem.MolType('W', [atomtypeW])
world = sim.chem.World([moltypeM, moltypeW], Dim = 3, Units = sim.units.AtomicUnits)
Sys = sim.system.System(world, Name = Prefix)
for i in range(NWater): Sys += moltypeW.New()
for i in range(NMethane): Sys += moltypeM.New()
Filter_MM = sim.atomselect.PolyFilter([atomtypeM, atomtypeM])
Filter_MW = sim.atomselect.PolyFilter([atomtypeM, atomtypeW])
Filter_WW = sim.atomselect.PolyFilter([atomtypeW, atomtypeW])
Filter_MW_LD = sim.atomselect.PolyFilter([atomtypeM, atomtypeW], Ordered = True)
Delta = 1.2
Pspline_MM = sim.potential.PairSpline(Sys, Filter = Filter_MM, Cut = 10.0, NKnot = 30, Label = "SP_MM")
Pspline_MW = sim.potential.PairSpline(Sys, Filter = Filter_MW, Cut = 10.0, NKnot = 30, Label = "SP_MW")
Pspline_WW = sim.potential.PairSpline(Sys, Filter = Filter_WW, Cut = 10.0, NKnot = 30, Label = "SP_WW")
Plocaldensity_MW = sim.potential.LocalDensity(Sys, Filter = Filter_MW_LD, Cut = LDCut, LowerCut = LDCut - Delta, NKnot = 30, RhoMin = 0., RhoMax = NMethane, Label = "LD")
if fixWW:
WWSPKnots = eval(file(os.path.expanduser('~/c25ld/c25_single_site_water/water_spce/spce_ff.dat')).read())
Pspline_WW.SetParam(Knots = WWSPKnots)
Sys.ForceField.extend([Pspline_MM, Pspline_MW, Pspline_WW, Plocaldensity_MW])
for P in Sys.ForceField: P.Arg.SetupHist(NBin = 1000, ReportNBin = 100)
#Sys.ForceField.SetSplineTreatment(NonbondEneSlope = 50., BondEneSlope = 10., AngleEneSlope = 60.)
for Pspline in [Pspline_MM, Pspline_MW, Pspline_WW]: Pspline.EneSlopeInner = None
Sys.Load()
Trj = pickleTraj(LammpsTraj)
Sys.BoxL = Trj.FrameData['BoxL']
Sys.TempSet = 298.0
sim.system.init.positions.CubicLatticeFill(Sys, Random = 0.1)
sim.system.init.velocities.Canonical(Sys, Temp = 298.0)
Int = Sys.Int
for Method in Int.Methods:
if hasattr(Method, 'TimeStep'): Method.TimeStep = 3.e-3
return Sys
def __init_MultiSrel(self, p, Sys, AATraj, cfg=None):
'''set Sys, Trj and Map for extended ensemble optimization'''
self.NTraj = len(AATraj)
self.p = p if isinstance(p, list) else [p] * self.NTraj
if cfg is None:
self.cfg = [x.cfg for x in self.p]
else:
self.cfg = cfg if isinstance(cfg, list) else [cfg] * self.NTraj
self.Sys = Sys if isinstance(Sys, list) else [Sys] * self.NTraj
self.Allp = self.p
self.AllSys = self.Sys
self.AATraj = AATraj
# list of pickled Trj objects
self.Trj = [pickleTraj(Traj) for Traj in self.AATraj]
# list of 1-1 maps (since all supplied trajs will be already mapped)
Map = [sim.atommap.PosMap() for i in range(self.NTraj)
] # need to create separate PosMap instances
for i in range(self.NTraj):
for (j, a) in enumerate(self.Sys[i].Atom):
Map[i] += [sim.atommap.AtomMap(Atoms1=j, Atom2=a)]
self.Map = Map
def runSrel(Sys):
Trj = pickleTraj(LammpsTraj, Verbose = True)
Map = sim.atommap.PosMap()
for (i, a) in enumerate(Sys.Atom): Map += [sim.atommap.AtomMap(Atoms1 = i, Atom2 = a)] #1:1 mapping since using a mapped traj
Int = Sys.Int
Int.Method = Int.Methods.VVIntegrate
Int.Method.Thermostat = Int.Method.ThermostatLangevin
Int.Method.LangevinGamma = 0.01
Sys.TempSet = 298.0
Pspline_MM = Sys.ForceField[0] ; Pspline_MW = Sys.ForceField[1] ; Pspline_WW = Sys.ForceField[2]
Plocaldensity = Sys.ForceField[-1]
PairPotentialList = [Pspline_MM, Pspline_MW] if fixWW else [Pspline_MM, Pspline_MW, Pspline_WW]
print "Resetting all potentials to base case"
for Pspline in PairPotentialList: Pspline.SetParam(Knots = 0.)
Plocaldensity.SetParam(Knots = 0.)
for p in Sys.ForceField: p.FreezeParam()
print Sys.ForceField.ParamString()
Opt = sim.srel.OptimizeTrajLammpsClass(Sys, Map, Traj = Trj, SaveLoadArgData = True, FilePrefix = Prefix, Verbose = True)
sim.srel.optimizetraj.PlotFmt = 'svg'
Opt.MinReweightFrac = 0.2
Opt.TempFileDir = os.getcwd()
opt_cases = ['SP', 'SPLD']
for i, case in enumerate(opt_cases):
Opt.Reset()
Opt.FilePrefix = Prefix + '_' + case
print "\n\nOptimizing for the case: ", case
if case == "SP":
for Pspline in PairPotentialList: Pspline.UnfreezeParam()
if case == "SPLD":
Plocaldensity.UnfreezeParam()
Sys.ForceField.Update()
Opt.RunConjugateGradient(StepsEquil = 10000000, StepsProd = 20000000, StepsStride = 500)
#write output headers
LDCuts = np.arange(4.5, 10.0, 0.1)
datalog = '%s_dSreldrc.dat' % datalog_prefix
if not os.path.isfile(datalog) or RefreshLogs:
of = open(datalog, 'w')
of.write('#LDCut \t dSreldrc\n')
of.close()
#various indexing schemes
TrjIter = {'AA': [0, -1, 10], 'CG': [0, -1, 10]}
# compile fortcode
fcompile()
from dSreldrc_fortlib import getdudrc
Trj_AA = pickleTraj(LammpsTraj)
BoxL = Trj_AA.FrameData['BoxL'][0]
#begin looping over different LD cutoffs
for i, LDCut in enumerate(LDCuts):
print '\n\nLDCut = %g\n' % LDCut
#calculate coefficients
(coeff, dcoeff) = alg.calcCoeff(LDCut = LDCut, Delta = 1.2)
#get AA and CG trj
Trj_CG = pickleTraj(base_fmt['cg_trj'] % (fftype, i))
#get Spline Coeffs for CG forcefield
ffield_CG = base_fmt['cg_ff'] % (fftype, i)
#!/usr/bin/env python
import os, pickle, sys
import numpy as np
import sim
import pickleTraj
LammpsTrajIn = os.path.abspath(sys.argv[1])
LammpsTrajOut = os.path.abspath(sys.argv[2])
Trj = pickleTraj(LammpsTrajIn)
BoxL = Trj.FrameData['BoxL']
monomer_atomname = '3'
mappedatoms = []
for (i,AtomType) in enumerate(Trj.AtomTypes):
if AtomType == int(monomer_atomname):
mappedatoms.append(i)
Map = sim.atommap.PosMap()
for (i,j) in enumerate(mappedatoms):
Map += [sim.atommap.AtomMap(Atoms1 = j, Atom2 = i, Atom2Name = monomer_atomname)]
AtomNames = [monomer_atomname] * len(mappedatoms)
MappedTrj = sim.traj.Mapped(Trj, Map, AtomNames = AtomNames)
sim.traj.Convert(MappedTrj, sim.traj.LammpsWrite, LammpsTrajOut, Verbose = True)
pickleTraj(LammpsTrajOut)
#input files
base_fmt = {'cg_ff': ff_fmtstring, 'cg_trj': md_fmtstring}
#output arrays
LDCuts = np.arange(4.5, 10.0, 0.1)
delta_Srel = {'Bennett': np.zeros([len(LDCuts), NBlocks], np.float64), 'Fep' : np.zeros([len(LDCuts), NBlocks], np.float64)}
datalog = {'Bennett': '%s_Srel_Bennett.dat' % datalog_prefix, 'Fep': '%s_Srel_Fep.dat' % datalog_prefix }
#various indexing schemes
poly_dict = SysData['poly_dict']
serial_index = {'AA': (0, poly_dict['N_mon']*poly_dict['N_poly']),
'CG': (0, poly_dict['N_mon']*poly_dict['N_poly'])} #always using a mapped traj
#extract all necessary AA data
Trj_AA = pickleTraj(LammpsTraj)
BoxL = Trj_AA.FrameData['BoxL']
#begin looping over different LD cutoffs
for i, LDCut in enumerate(LDCuts[0:-1]):
print '\n\nLDCUTs = (%g, %g)\n' % (LDCuts[i], LDCuts[i+1])
#extract all necessary CG data
sumfile1 = base_fmt['cg_ff'] % (fftype, i); sumfile2 = base_fmt['cg_ff'] % (fftype, (i+1))
trajfile1 = base_fmt['cg_trj'] % (fftype, i) ; trajfile2 = base_fmt['cg_trj'] % (fftype, (i+1))
ParamString1 = parse_potential.parseParamString(sumfile1); ParamString2 = parse_potential.parseParamString(sumfile2)
Trj_CG_1 = pickleTraj(trajfile1); Trj_CG_2 = pickleTraj(trajfile2)
#create systems with forcefields of LDCuts i and i+1
Sys1 = alg.makeSys(LDCut = LDCuts[i], Delta = Delta, BoxL = BoxL, fftype = fftype, Prefix = 'bennettsys1',
TrajFn = FMT['TRAJ'] % (TrajPrefix, TempSet) # fancy intro print 'ANALYSING MULTI-PROTEIN FOR %s at %3.2f K' % (Prefix, TempSet) print '----------------------------------------------------------------' # set up Compute object print 'Creating Compute object' calc = cg.Compute(NativePdb = NativePdb, TrajFn = TrajFn, Temp = TempSet, Prefix = OutPrefix, hasPseudoGLY = hasPseudoGLY) # cluster the room temp traj print 'Clustering trajectory' calc.Cluster() # top-cluster contact analysis Trj = pickleTraj(TrajFn) BoxL = Trj.FrameData['BoxL'] ClustPdb = FMT['CLUSTPDB'] % (calc.Prefix, calc.Temp) p = cg.ProteinNCOS(ClustPdb, Model = 1) # top cluster contact map print 'Calculating contact map for top cluster' cmap, cdist = p.GetResContacts(BoxL = BoxL) picklename = FMT['RESCONTACTS'] % (calc.Prefix + '_topclust', calc.Temp) with open(picklename, 'w') as of: pickle.dump(cmap, of) # top cluster dihedrals print 'Calculating dihedral angles for top cluster' Phi, Psi = p.GetPhiPsi(BoxL = BoxL) picklename = FMT['RAMA'] % (calc.Prefix + '_topclust', calc.Temp) with open(picklename, 'w') as of: pickle.dump((Phi, Psi), of)
if isPolymer:
NStep = NStep_polymer
else:
NStep = NStep_methane
#system parameters
SysData = alg.makeSysData(isPolymer = isPolymer, hasLJ = hasLJ, N_mon = N_mon, N_water = N_water)
TempSet = 298.0
Delta = 1.2
#CG forcefield parameters
cg_ff_file = cgffPrefix + '_sum.txt'
paramstring = pp.parseParamString(cg_ff_file)
#boxlength extracted from AA traj
BoxL = pickleTraj(LammpsTraj).FrameData['BoxL']
#create the system object
Sys = alg.makeSys(LDCut = LDCut, SysData = SysData, fftype = fftype, BoxL = BoxL, Prefix = Prefix, paramstring = paramstring, Delta = 1.2)
#initialize system
sim.system.init.positions.CubicLattice(Sys, Random = 0.1)
sim.system.init.velocities.Canonical(Sys, Temp = TempSet)
##different MD steps
Int = Sys.Int
#energy minimization
print 'Minimizing energy...'
Int.Method = Int.Methods.VVQuench
Int.Run(NStep['Min'])
cfg = cg.config.Config()
cfg.AtomS['GLY'] = cg.const.AtomS_GLY
p = cg.topo.ProteinNCOS(Pdb=pdbfile, cfg=cfg, Prefix='protg_test')
ret = cg.parsestruct.ParsePdb(p)
c_nonnative = ret['c_nonnative']
x, y = zip(*c_nonnative)
resnums = list(x) + list(y)
resnums = list(set(resnums))
SInds_nonnative = p.GetSInds(ResNums=resnums)
d_nonnative_pdb = ret['d_nonnative']
d_ss_nonnative_pdb = ret['d_ss_nonnative']
trj = pickleTraj(trajfile)
NFrames = len(trj)
if not os.path.isfile('protg_traj_nonnative_ss.txt'):
d_ss_nonnative_traj = np.zeros([NFrames, len(c_nonnative)])
pb = sim.utility.ProgressBar(
Text='Calculating s-s distances for non-native contacts...',
Steps=NFrames * len(c_nonnative))
count = 0
for n in range(NFrames):
Pos = trj[n]
for k, (i, j) in enumerate(c_nonnative):
si = SInds_nonnative[i]
sj = SInds_nonnative[j]
d_si_sj = Pos[sj] - Pos[si]
d = np.sqrt(np.sum(d_si_sj * d_si_sj))
d_ss_nonnative_traj[n, k] = d
if reftable[i,0] == float(conc):
NB = reftable[i,1]
NW = reftable[i,2]
BoxL = reftable[i,3]
# parse filenames
xyzTrj_original = os.path.join(srcDir, 'conc_%s' % conc, 'CG_trajectory_%s.xyz' % conc)
xyzTrj = os.path.join(tarDir, 'NB%dNW%d' % (NB,NW), 'CG_trajectory_%s.xyz' % conc)
LammpsTrj = os.path.join(tarDir, 'NB%dNW%d' % (NB,NW), 'NB%dNW%d_prod.lammpstrj' % (NB, NW))
TCLFile = os.path.join(tarDir, 'NB%dNW%d' % (NB, NW), 'conv_xyz.tcl')
# copy traj to required location and unzip it
if not os.path.isdir(os.path.join(tarDir, 'NB%dNW%d' % (NB, NW))): os.mkdir(os.path.join(tarDir, 'NB%dNW%d' % (NB, NW)))
os.system('cp %s %s' % (xyzTrj_original, xyzTrj))
# run vmd
VMDExec = '/home/cask0/home/tsanyal/software/tanmoy_vmd/vmd'
VMDParams = {'xyz' : xyzTrj.split('/')[-1], 'lammpstrj': LammpsTrj.split('/')[-1], 'boxl': BoxL}
file(TCLFile, 'w').write(tclscript % VMDParams)
os.chdir(os.path.join(tarDir, 'NB%dNW%d' % (NB, NW)))
os.system('%s -dispdev text -e %s' % (VMDExec, TCLFile))
os.system('gzip %s' % LammpsTrj)
os.chdir(curr_dir)
# pickle final traj
pickleTraj(LammpsTrj+'.gz', Verbose = True)
if DelTempFiles:
[os.remove(x) for x in [TCLFile, xyzTrj]]
# test system of 5 benzene and 10 waters cg.doMinimize = False cg.NB = 5 cg.NW = 10 cg.LammpsTraj = '/home/cask0/home/tsanyal/benwat/data/gromacs/NB50NW450/NB50NW450_prod.lammpstrj.gz' cg.Prefix = 'matchEne' # local density potential params cg.LDCutBW = 7.5 # can change to BB, WW, BW etc to experiment cg.LD_Delta = 1.2 cg.RhoMin = 0 cg.RhoMax = cg.NB testLDKnots = 2 * (1 - 0.3 * np.linspace(0, cg.NB, cg.NLDKnots)) # box length LammpsTrj = pickleTraj(cg.LammpsTraj, Verbose = True) cg.BoxL = LammpsTrj.FrameData['BoxL'] print 'Making system...' Sys = cg.makeSys() sumfile = '/home/cask0/home/tsanyal/benwat/data/cgff/NB50NW450_init/NB50NW450_SP_sum.txt' # load in converged pair splines or 0 pair potential from NB50NW450 and test LD Knots SP_BB = Sys.ForceField[0] ; SP_WW = Sys.ForceField[1] ; SP_BW = Sys.ForceField[2] LD = Sys.ForceField[-1] for P in [SP_BB, SP_WW, SP_BW]: P.SetParam(Knots = [0.] * cg.NSPKnots) #P.SetParam(**pp.parseParam(sumfile, P.Name)) LD.SetParam(Knots = testLDKnots) Sys.ForceField.Update() Sys.TempSet = 300.0 sim.system.init.positions.CubicLatticeFill(Sys, Random = 0.1) sim.system.init.velocities.Canonical(Sys, Temp = 298.0) Int = Sys.Int Sys.Measures.VerboseOutput(StepFreq = 100)
TrjName = GromacsTrj.split('/')[-1]
LammpsData = os.path.join(TrjDir, 'temp.data')
LammpsTrj = GromacsTrj.split('.')[0] + '_unmapped.lammpstrj'
TCLFile = os.path.join(TrjDir, 'conv_trj.tcl')
# run vmd
VMDExec = '/home/cask0/home/tsanyal/software/tanmoy_vmd/vmd'
VMDParams = {'gro' : GromacsStruct, 'xtc': GromacsTrj,'lammpstrj': LammpsTrj}
file(TCLFile, 'w').write(tclscript % VMDParams)
os.system('%s -dispdev text -e %s' % (VMDExec, TCLFile))
os.system('gzip %s' % LammpsTrj)
# map traj using sim
LammpsTrjIn = LammpsTrj + '.gz'
LammpsTrjOut = GromacsTrj.split('.')[0] + '.lammpstrj.gz'
Trj = pickleTraj(LammpsTrjIn, Verbose = False)
BoxL = Trj.FrameData['BoxL']
Map = sim.atommap.PosMap()
# vmd created lammpstraj places all benzene atoms at the beginning in (C1,H1,C2,H2,...) sequence
MassList_B = [12.011, 1.008] * 6
for i in range(0, NB): Map += [sim.atommap.AtomMap(Atoms1 = range(i*12, (i+1)*12), Atom2 = i, Mass1 = MassList_B)]
for i in range(0, NW): Map += [sim.atommap.AtomMap(Atoms1 = NB*12 + i, Atom2 = NB+i)]
AtomTypes = [1]*NB + [2]*NW
MappedTrj = sim.traj.Mapped(Trj, Map, AtomNames = AtomTypes, BoxL = BoxL)
sim.traj.Convert(MappedTrj, sim.traj.LammpsWrite, LammpsTrjOut, Verbose = True)
# pickle final traj
pickleTraj(LammpsTrjOut, Verbose = True)
if DelTempFiles: os.remove(TCLFile)
traj = os.path.abspath(sys.argv[1])
fftype = sys.argv[2]
nmethanes = int(sys.argv[3])
prefix = sys.argv[4]
savedir = sys.argv[5]
## check if computation needs to be done
if not os.path.isdir(os.path.join(savedir, 'measure')): os.mkdir(os.path.join(savedir, 'measure'))
if not os.path.isdir(os.path.join(savedir, 'hist')): os.mkdir(os.path.join(savedir, 'hist'))
measurepickleName = os.path.join(savedir, 'measure', prefix + '.pickle')
histpickleName = os.path.join(savedir, 'hist', prefix + '.pickle')
if os.path.isfile(histpickleName):
quit()
## pickle trajectory
trj = pickleTraj(traj)
## frame-selector
start = 0; stop = len(trj); freq = 10
frame_range = range(start,stop,freq)
nframes = len(frame_range)
## Initialise trajectory reader and read parameters
boxl = trj.FrameData['BoxL']
## make bins
bin_centers = range(0, nmethanes+1)
bin_vals = np.zeros([nframes, nmethanes+1], np.float64)
bin_val_final = np.zeros(nmethanes+1)
## frame stepping
#/usr/bin/env python
import os, sys
import numpy as np
import pickleTraj
sys.path.append('../')
import cgmodel
cgmodel.doMinimize = False
cgmodel.NB = 50 ; cgmodel.NW = 450
cgmodel.LDCutBW = 7.8
cgmodel.LammpsTraj = '/home/cask0/home/tsanyal/benwat/data/gromacs/NB50NW450/NB50NW450_npt.lammpstrj.gz'
cgmodel.Prefix = 'test'
trj = pickleTraj(cgmodel.LammpsTraj, Verbose = True)
cgmodel.BoxL = trj.FrameData['BoxL']
Sys = cgmodel.makeSys()
cgmodel.runSrel(Sys = Sys)
#!/usr/bin/env python import sim import sys import pickleTraj LammpsTrjIn = sys.argv[1] LammpsTrjOut = sys.argv[2] N_mon = int(sys.argv[3]) N_water = int(sys.argv[4]) Trj = pickleTraj(LammpsTrjIn, Verbose = False) BoxL = Trj.FrameData['BoxL'] Map = sim.atommap.PosMap() for i in range(0, N_water): Map += [sim.atommap.AtomMap(Atoms1 = i*3+2, Atom2= i)] for i in range(0, N_mon): Map += [sim.atommap.AtomMap(Atoms1 = 3*N_water + i, Atom2 = N_water + i)] AtomTypes = [1]*N_water + [2]*N_mon MappedTrj = sim.traj.Mapped(Trj, Map, AtomNames = AtomTypes) sim.traj.Convert(MappedTrj, sim.traj.LammpsWrite, LammpsTrjOut, Verbose = True)
sys.path.append('/home/cask0/home/tsanyal/benwat')
import cgmodel as cg
#TODO: populate these lists with distinct values for the different lammpstraj
# or with same value (need to enquire with Scott)
LDCutBB = []
LDCutBW = []
Temp = 300
cg.TempSet = Temp
cg.LammpsTraj = LammpsTraj
cg.Prefix = 'NB%dNW%d_multi' % (NB, NW)
cg.LDCutBB = LDCutBB
cg.LDCutBW = LDCutBW
trj = pickleTraj(LammpsTraj, Verbose = True)
cg.BoxL = trj.FrameData['BoxL']
Sys = cg.makeSys()
TrajList = []
NMol = 500
NBList = [50,100,150,200,250,300,350,400,450,500]
NWList = [] ; [NWList.append(500-x) for x in NBList]
for i, NB in enumerate(NBList):
NW = NWList[i]
Traj = os.path.join('/home/cask0/home/tsanyal/benwat/data/gromacs/NB%dNW%d/NB%dNW%d_prod.lammpstrj.gz'
% (NB, NW))
TrajList.append(Traj)
cg.MultiLammpsTraj = TrajList
#check if already computed LogFileName = '/home/cask0/home/tsanyal/c25ld/nov15_runs_new_rc/geom_prop/energy_logs/%s_energy.pickle' % Prefix #if os.path.isfile(LogFileName): exit() #system parameters SysData = alg.makeSysData(isPolymer = isPolymer, hasLJ = hasLJ, N_mon = N_mon, N_water = N_water) TempSet = 298.0 Delta = 1.2 #CG forcefield parameters cg_ff_file = cgffPrefix + '_sum.txt' paramstring = pp.parseParamString(cg_ff_file) #boxlength extracted from AA traj Trj = pickleTraj(LammpsTraj) BoxL = Trj.FrameData['BoxL'] #create the system object Sys = alg.makeSys(LDCut = LDCut, SysData = SysData, fftype = fftype, BoxL = BoxL, Prefix = Prefix, paramstring = paramstring, Delta = 1.2) Sys.TempSet = TempSet Int = Sys.Int Int.Method = Int.Methods.VVIntegrate Int.Method.Thermostat = Int.Method.ThermostatLangevin Int.Method.LangevinGamma = 0.01 #if calcAtomEne and DEBUG: Sys_test = copy.deepcopy(Sys) # Extract potential objects Plj = None; Pspline = None ; Plocaldensity = None if hasLJ:
