def createBasinHopping(self):
GMIN.initialize()
pot = gminpot.GMINPotental(GMIN)
coords = pot.getCoords()
step = displace.RandomDisplacement()
opt = bh.BasinHopping(coords, pot, takeStep=step, temperature=0.4, storage=self.storage)
return opt
def __init__(self, prmtopFname, inpcrdFname ): # prmtopFname, inpcrdFname ):
# reads coords.inpcrd , coords.prmtop , min.in and data
# - fnames hard coded (todo)
super(GMINAmberPotential, self).__init__(GMIN)
# self.potentialLocal = gminpot.GMINPotential(GMIN)
GMIN.initialize()
self.prmtop = AmberPrmtopFile( prmtopFname )
self.inpcrd = AmberInpcrdFile( inpcrdFname )
# number of atoms
self.natoms = self.prmtop.topology._numAtoms
self.localCoords = self.inpcrd.positions/angstrom
def __init__(self, prmtopFname, inpcrdFname): # prmtopFname, inpcrdFname ):
# reads coords.inpcrd , coords.prmtop , min.in and data
# - fnames hard coded (todo)
super(GMINAmberPotential, self).__init__(GMIN)
# self.potentialLocal = gminpot.GMINPotential(GMIN)
GMIN.initialize()
self.prmtop = AmberPrmtopFile(prmtopFname)
self.inpcrd = AmberInpcrdFile(inpcrdFname)
# number of atoms
self.natoms = self.prmtop.topology._numAtoms
self.localCoords = self.inpcrd.positions / angstrom
# cg
# ret = cg( coordsVec, pot.getEnergyGradient)
# runtime error -- ValueError: The truth value of an array with more than ...
# fire
retOpmm = fire(coordsVec, pot, tol=1e-3, nsteps=1000)
# works but quenched energy is higher!
print("quenched energy ", retOpmm.energy)
print("rms gradient", retOpmm.rms)
print("number of function calls", retOpmm.nfev)
# -------- GMIN
print("\n\nCompare with GMIN")
GMIN.initialize() # reads coords.inpcrd and coords.prmtop
pot = gminpot.GMINPotential(GMIN)
coords = pot.getCoords()
enerGmin = pot.getEnergy(coords)
egmin, gminEGrad = pot.getEnergyGradient(coords)
retGmin = fire(coords, pot, tol=1e-3, nsteps=1000)
print(" -- pre-quench --")
print("E gmin : ", egmin)
print(" openmm: ", eo / 4.184)
print("grad gmin : ", gminEGrad[0:3])
print(" openmm: ", go[0:3] / 41.84)
# cg
# ret = cg( coordsVec, pot.getEnergyGradient)
# runtime error -- ValueError: The truth value of an array with more than ...
# fire
retOpmm = fire( coordsVec, pot, tol = 1e-3, nsteps=1000)
# works but quenched energy is higher!
print "quenched energy ", retOpmm.energy
print "rms gradient", retOpmm.rms
print "number of function calls", retOpmm.nfev
# -------- GMIN
print "\n\nCompare with GMIN"
GMIN.initialize() # reads coords.inpcrd and coords.prmtop
pot = gminpot.GMINPotential(GMIN)
coords = pot.getCoords()
enerGmin = pot.getEnergy(coords)
egmin,gminEGrad = pot.getEnergyGradient(coords)
retGmin = fire( coords, pot, tol = 1e-3, nsteps=1000)
print " -- pre-quench --"
print "E gmin : ", egmin
print " openmm: ", eo/4.184
print "grad gmin : ", gminEGrad[0:3]
print " openmm: ", go[0:3]/41.84
import ambgmin_ as GMIN
import pele.potentials.gminpotential as gminpot
import numpy as np
import pele.basinhopping as bh
from pele.optimize import _quench as quench
from pele.takestep import displace
# export PYTHONPATH=/home/ss2029/svn/GMIN/bin:$PWD/../..
GMIN.initialize()
pot = gminpot.GMINPotental(GMIN)
coords = pot.getCoords()
step = displace.RandomDisplacement(stepsize=0.7)
opt = bh.BasinHopping(coords, pot, takeStep=step, quenchRoutine=quench.lbfgs_py)
opt.quenchParameters['tol'] = 1e-4
opt.run(3)
# some visualization
try:
import pele.utils.pymolwrapper as pym
pym.start()
pym.draw_spheres(opt.coords, "A", 1)
except:
print "Could not draw using pymol, skipping this step"
from pele.utils.xyz import write_xyz
write_xyz(open("final.xyz", "w"), opt.coords)
import ambgmin_ as GMIN
import pygmin.potentials.gminpotential as gminpot
import numpy as np
import pygmin.basinhopping as bh
from pygmin.optimize import _quench as quench
from pygmin.takestep import displace
# export PYTHONPATH=/home/ss2029/svn/GMIN/bin:$PWD/../..
GMIN.initialize()
pot = gminpot.GMINPotental(GMIN)
coords = pot.getCoords()
step = displace.RandomDisplacement(stepsize=0.7)
opt = bh.BasinHopping(coords,
pot,
takeStep=step,
quenchRoutine=quench.lbfgs_py)
opt.quenchParameters['tol'] = 1e-4
opt.run(3)
# some visualization
try:
import pygmin.utils.pymolwrapper as pym
pym.start()
pym.draw_spheres(opt.coords, "A", 1)
except:
print "Could not draw using pymol, skipping this step"
import pygmin.printing.print_atoms_xyz as pr
def __init__(self):
self.storage = savenlowest.SaveN(10)
GMIN.initialize()