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src/p/e/pele-HEAD/examples/amber/metenk/run_gui.py   pele(Download)
import numpy as np
import time
import pele.utils.readAmberParam as readAmb
import ambgmin_ as GMIN
import pele.potentials.gminpotential as gminpot
    def createBasinHopping(self):
        GMIN.initialize()   
        pot = gminpot.GMINPotental(GMIN)
        coords = pot.getCoords()
 
    def createNEB(self, coords1, coords2):
        pot = gminpot.GMINPotental(GMIN)
        return NEB.NEB(coords1, coords2, pot, k = 100. ,nimages=20)
 
 

src/p/e/pele-HEAD/examples/amber/metenk/amber.py   pele(Download)
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
 
GMIN.initialize()   
pot = gminpot.GMINPotental(GMIN)
 
coords = pot.getCoords()

src/p/e/pele-HEAD/examples/amber/gmin_vs_openmm.py   pele(Download)
"""
 
import ambgmin_ as GMIN
import pele.potentials.gminpotential as gminpot
 
# energy from GMIN 
GMIN.initialize()   # reads coords.inpcrd and coords.prmtop 
pot = gminpot.GMINPotential(GMIN)
 
coords = pot.getCoords()

src/p/e/pele-HEAD/examples/amber/compare_with_ambgmin/OpenmmAmbPot.py   pele(Download)
import ambgmin_ as GMIN
import pele.potentials.gminpotential as gminpot
from pele.optimize import fire 
 
import numpy as np
    print "\n\nCompare with GMIN"    
    GMIN.initialize()   # reads coords.inpcrd and coords.prmtop 
    pot = gminpot.GMINPotential(GMIN)
 
    coords = pot.getCoords()

src/p/e/pele-HEAD/examples/amber/compare_with_ambgmin/ambEnergy.py   pele(Download)
import ambgmin_ as GMIN
import pele.potentials.gminpotential as gminpot
 
# OpenMM 
from simtk.openmm.app import * # AmberPrmtopFile, AmberInpcrdFile, PDBFile, Simulation
# energy from GMIN 
GMIN.initialize()   # reads coords.inpcrd and coords.prmtop 
pot = gminpot.GMINPotential(GMIN)
 
coords = pot.getCoords()

src/p/e/pele-HEAD/pele/amber/gmin_potential.py   pele(Download)
 
from pele.potentials import BasePotential
import ambgmin_ as GMIN 
from pele.potentials.gminpotential import GMINPotential
 
    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)