def report(self, sim, state):
"""Generate a report.
Parameters
----------
sim : :class:`app.Simulation`
The Simulation to generate a report for
state : :class:`mm.State`
The current state of the simulation
"""
global VELUNIT
crds = state.getPositions().value_in_unit(u.angstrom)
if self.rst7 is None:
self.uses_pbc = sim.topology.getUnitCellDimensions() is not None
self.atom = len(crds)
# First time written
self.rst7 = Rst7(
natom=self.atom,
title='Restart file written by ParmEd with OpenMM')
self.rst7.time = state.getTime().value_in_unit(u.picosecond)
flatcrd = [0.0 for i in xrange(self.atom * 3)]
for i in xrange(self.atom):
i3 = i * 3
flatcrd[i3], flatcrd[i3 + 1], flatcrd[i3 + 2] = crds[i]
self.rst7.coordinates = flatcrd
if self.write_velocities:
vels = state.getVelocities().value_in_unit(VELUNIT)
flatvel = [0.0 for i in xrange(self.atom * 3)]
for i in xrange(self.atom):
i3 = i * 3
flatvel[i3], flatvel[i3 + 1], flatvel[i3 + 2] = vels[i]
self.rst7.vels = flatvel
if self.uses_pbc:
boxvecs = state.getPeriodicBoxVectors()
lengths, angles = box_vectors_to_lengths_and_angles(*boxvecs)
lengths = lengths.value_in_unit(u.angstrom)
angles = angles.value_in_unit(u.degree)
self.rst7.box = [
lengths[0], lengths[1], lengths[2], angles[0], angles[1],
angles[2]
]
if self.write_multiple:
fname = self.fname + '.%d' % sim.currentStep
else:
fname = self.fname
self.rst7.write(fname, self.netcdf)
def get_U_invU(asu_rst7_file_name): rst7 = Rst7.open(asu_rst7_file_name) UCbox = rst7.box U, invU = raf.CompXfrm(UCbox) return U, invU, UCbox
#! /usr/bin/env python
import sander
from chemistry.amber.readparm import AmberParm, Rst7
import numpy as np
pdb = '3stl'
parm = AmberParm('4amber_%s.prmtop' % pdb) #topo
rst = Rst7.open('4amber_%s.rst7' % pdb) #box
sander.setup(parm, rst.coordinates, rst.box, sander.pme_input())
ene, frc = sander.energy_forces()
print ene.tot
print max(frc)
import code
code.interact(local=dict(globals(), **locals()))
sander.cleanup()
#! /usr/bin/env python
import sander
from chemistry.amber.readparm import AmberParm, Rst7
import numpy as np
pdb ='3stl'
parm = AmberParm('4amber_%s.prmtop' %pdb) #topo
rst = Rst7.open('4amber_%s.rst7' %pdb) #box
sander.setup(parm, rst.coordinates, rst.box, sander.pme_input())
ene, frc = sander.energy_forces()
print ene.tot
print max(frc)
import code; code.interact(local=dict(globals(), **locals()))
sander.cleanup()
def get_U_invU(asu_rst7_file_name):
rst7 = Rst7.open(asu_rst7_file_name)
UCbox = rst7.box
U, invU = raf.CompXfrm(UCbox)
return U, invU, UCbox
#! /usr/bin/env python
import sander
from chemistry.amber.readparm import AmberParm, Rst7
from chemistry.structure import Structure, read_PDB, write_PDB
import numpy as np
parm = AmberParm('4amber_1cby.prmtop')
pdb = read_PDB('new.pdb')
rst = Rst7.open('4amber_1cby.rst7')
xyz = pdb.pdbxyz[0]
sander.setup(parm,xyz, rst.box, sander.pme_input())
sander.set_positions(xyz)
ene, frc = sander.energy_forces()
#~ import code; code.interact(local=dict(globals(), **locals()))
sander.cleanup()
