Example #1
0
    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
Example #2
0
    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
Example #3
0
    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
Example #4
0
    # 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)
Example #5
0
    # 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
Example #6
0
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)
Example #7
0
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
Example #8
0
 def __init__(self):
     self.storage = savenlowest.SaveN(10)
     GMIN.initialize()