rdf.add(MolIdx(0) + AtomName("O00"), AtomName("O00"))
rdf2 = RDFMonitor(0 * angstrom, 10 * angstrom, 0.05 * angstrom)
rdf2.add(MolIdx(0) + AtomName("O00"), AtomName("H01"))
rdf2.add(MolIdx(0) + AtomName("O00"), AtomName("H02"))
system.add(cljff)
system.add("O-O RDF", rdf)
system.add("O-H RDF", rdf2)
t.start()
system.collectStats()
ms = t.elapsed()
print("Collecting stats took %d ms" % ms)
rdf = system.monitor(MonitorName("O-O RDF"))
print("\nO-O RDF")
for i in range(0, rdf.nBins()):
print(rdf[i].middle().to(angstrom), rdf[i].value())
rdf = system.monitor(MonitorName("O-H RDF"))
print("\nO-H RDF")
for i in range(0, rdf.nBins()):
print(rdf[i].middle().to(angstrom), rdf[i].value())
# output="BOND-A1A2.dat")
#histoAnalysis(nbins=nbins,
# avgnrg = system.monitor( MonitorName("total_energy") ).accumulator().average(),
# values=system.monitor( MonitorName("bond23") ).accumulator().values(),
# mode="bond",
# output="BOND-A2A3.dat")
#histoAnalysis(nbins=nbins,
# avgnrg = system.monitor( MonitorName("total_energy") ).accumulator().average(),
# values=system.monitor( MonitorName("bond34") ).accumulator().values(),
# mode="bond",
# output="BOND-A3A4.dat")
#histoAnalysis(nbins=nbins,
# avgnrg = system.monitor( MonitorName("total_energy") ).accumulator().average(),
# values=system.monitor( MonitorName("theta123") ).accumulator().values(),
# mode="angle",
# output="ANGLE-A1A2A3.dat")
#histoAnalysis(nbins=nbins,
# avgnrg = system.monitor( MonitorName("total_energy") ).accumulator().average(),
# values=system.monitor( MonitorName("theta234") ).accumulator().values(),
# mode="angle",
# output="ANGLE-A2A3A4.dat")
histoAnalysis(nbins=nbins,
avgnrg = system.monitor( MonitorName("total_energy") ).accumulator().average(),
values=list(system.monitor( MonitorName("phi1234") ).accumulator().values()),
mode="angle",
output="DIHEDRAL-A1A2A3A4.dat")
#** Output the trajectory
#system.monitor( MonitorName("trajectory") ).writeToDisk("outputXXXXXX.pdb")
.setProperty("b-factor",beta_ljnrg).molecule().commit()
total_mol = total_mol.atom(atoms[j].index()).edit() \
.setProperty("b-factor",beta_total).molecule().commit()
coul_group.update(coul_mol)
lj_group.update(lj_mol)
total_group.update(total_mol)
print("Total energies: %f %f %f" % (cnrg, ljnrg, cnrg + ljnrg))
PDB().write(coul_group, "test_coul_%0004d.pdb" % id)
PDB().write(lj_group, "test_lj_%0004d.pdb" % id)
PDB().write(total_group, "test_total_%0004d.pdb" % id)
print("Running a simulation...")
for i in range(1, 11):
system = moves.move(system, 2000, True)
nrgmon = system.monitor(MonitorName("solute_shell"))
PDB().write(system.molecules(), "test_sim_%0004d.pdb" % i)
system.clearStatistics()
print("Step %d of 10: Energy = %s" % (i, system.energy()))
view(nrgmon, i)
rdf2 = RDFMonitor( 0*angstrom, 10*angstrom, 0.05*angstrom )
rdf2.add( MolIdx(0) + AtomName("O00"), AtomName("H01") )
rdf2.add( MolIdx(0) + AtomName("O00"), AtomName("H02") )
system.add(cljff)
system.add("O-O RDF", rdf)
system.add("O-H RDF", rdf2)
t.start()
system.collectStats()
ms = t.elapsed()
print("Collecting stats took %d ms" % ms)
rdf = system.monitor( MonitorName("O-O RDF") )
print("\nO-O RDF")
for i in range(0,rdf.nBins()):
print(rdf[i].middle().to(angstrom), rdf[i].value())
rdf = system.monitor( MonitorName("O-H RDF") )
print("\nO-H RDF")
for i in range(0,rdf.nBins()):
print(rdf[i].middle().to(angstrom), rdf[i].value())
t = QTime()
t.start()
# Run the simulation
for i in range(0, nblocks):
print("Running nmove...")
t.restart()
system = moves.move(system, nmoves, True)
print("...took %d ms" % t.elapsed())
print("Analysis...")
# make an histogram...
nbins = 31
histoAnalysis(
nbins=nbins,
values=list(system.monitor(MonitorName("bond12")).accumulator().values()),
mode="bond",
output="BOND-A1A2.dat")
histoAnalysis(
nbins=nbins,
values=list(system.monitor(MonitorName("bond23")).accumulator().values()),
mode="bond",
output="BOND-A2A3.dat")
histoAnalysis(nbins=nbins,
values=list(
system.monitor(
MonitorName("angle123")).accumulator().values()),
mode="angle",
output="ANGLE-A1A2A3.dat")
lj_mol = lj_mol.atom(atoms[j].index()).edit() \
.setProperty("b-factor",beta_ljnrg).molecule().commit()
total_mol = total_mol.atom(atoms[j].index()).edit() \
.setProperty("b-factor",beta_total).molecule().commit()
coul_group.update(coul_mol)
lj_group.update(lj_mol)
total_group.update(total_mol)
print("Total energies: %f %f %f" % (cnrg, ljnrg, cnrg+ljnrg))
PDB().write(coul_group, "test_coul_%0004d.pdb" % id)
PDB().write(lj_group, "test_lj_%0004d.pdb" % id)
PDB().write(total_group, "test_total_%0004d.pdb" % id)
print("Running a simulation...")
for i in range(1,11):
system = moves.move(system, 2000, True)
nrgmon = system.monitor( MonitorName("solute_shell") )
PDB().write(system.molecules(), "test_sim_%0004d.pdb" % i)
system.clearStatistics()
print("Step %d of 10: Energy = %s" % (i, system.energy()))
view(nrgmon, i)
break
moves = SameMoves(solute_mover)
print("Production")
for i in range(0,nblocks):
print("Running block %d " % i)
system = moves.move(system, nmoves, True)
#sys.exit(-1)
print("Analysis...")
# make an histogram...
nbins=31
for bond in var_bonds:
bmonitor = "b_%s_%s" % (bond.atom0().value(),bond.atom1().value())
histoAnalysis(nbins=nbins,
values=list(system.monitor( MonitorName(bmonitor) ).accumulator().values()),
avgnrg = system.monitor( MonitorName("total_energy") ).accumulator().average(),
mode="bond",
output="BOND-%s.dat" % bmonitor)
for angle in var_angles:
amonitor = "a_%s_%s_%s" % (angle.atom0().value(),
angle.atom1().value(),
angle.atom2().value() )
histoAnalysis(nbins=nbins,
values=list(system.monitor( MonitorName(amonitor) ).accumulator().values()),
avgnrg = system.monitor( MonitorName("total_energy") ).accumulator().average(),
mode="angle",
output="ANGLE-%s.dat" % amonitor)
t = QTime()
t.start()
# Run the simulation
for i in range(0,nblocks):
print("Running nmove...")
t.restart()
system = moves.move(system, nmoves, True)
print("...took %d ms" % t.elapsed())
print("Analysis...")
# make an histogram...
nbins=31
histoAnalysis(nbins=nbins,
values=list(system.monitor( MonitorName("bond12") ).accumulator().values()),
mode="bond",
output="BOND-A1A2.dat")
histoAnalysis(nbins=nbins,
values=list(system.monitor( MonitorName("bond23") ).accumulator().values()),
mode="bond",
output="BOND-A2A3.dat")
histoAnalysis(nbins=nbins,
values=list(system.monitor( MonitorName("angle123") ).accumulator().values()),
mode="angle",
output="ANGLE-A1A2A3.dat")
#** Output the trajectory
#system.monitor( MonitorName("trajectory") ).writeToDisk("outputXXXXXX.pdb")
e_total = system.totalComponent()
system.add( "total_energy", MonitorComponent(e_total, Average()) )
#system.add( "trajectory", TrajectoryMonitor(system[MGIdx(0)]), 1 )
# Run the simulation
for i in range(0,nblocks):
print("Running nmove...")
system = moves.move(system, nmoves, True)
print("Analysis...")
# make an histogram...
nbins=31
histoAnalysis(nbins=nbins,
values=list(system.monitor( MonitorName("bond12") ).accumulator().values()),
avgnrg = system.monitor( MonitorName("total_energy") ).accumulator().average(),
mode="bond",
output="BOND-A1A2.dat")
histoAnalysis(nbins=nbins,
values=list(system.monitor( MonitorName("bond23") ).accumulator().values()),
avgnrg = system.monitor( MonitorName("total_energy") ).accumulator().average(),
mode="bond",
output="BOND-A2A3.dat")
histoAnalysis(nbins=nbins,
values=list(system.monitor( MonitorName("angle123") ).accumulator().values()),
avgnrg = system.monitor( MonitorName("total_energy") ).accumulator().average(),
mode="angle",
output="ANGLE-A1A2A3.dat")
#** Output the trajectory