.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)
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)
