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import numpy as np | |
from scipy.optimize.minpack import _lazywhere, _relerr | |
def fixed_point_zhou(func, x0, args=(), xtol=1E-14, maxiter=100000, p=6, rcond=1E-6): | |
""" | |
Find a fixed point of the function. | |
Given a function of one or more variables and a starting point, find a | |
fixed-point of the function: i.e. where ``func(x0) == x0``. |
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import simtk.openmm.app as app | |
import numpy as np | |
import simtk.openmm as mm | |
from simtk import unit as u | |
from openmmtools import integrators, testsystems | |
temperature = 300 * u.kelvin | |
testsystem = testsystems.WaterBox() |
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#!/bin/bash | |
#set -x | |
# Shows you the largest objects in your repo's pack file. | |
# Written for osx. | |
# | |
# @see http://stubbisms.wordpress.com/2009/07/10/git-script-to-show-largest-pack-objects-and-trim-your-waist-line/ | |
# @author Antony Stubbs | |
# set the internal field spereator to line break, so that we can iterate easily over the verify-pack output |
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import mdtraj as md | |
import simtk.openmm.app as app | |
import pdbfixer | |
fixer = pdbfixer.PDBFixer(pdbid='4fmu') | |
fixer.findMissingResidues() | |
fixer.findNonstandardResidues() | |
fixer.replaceNonstandardResidues() | |
fixer.findMissingAtoms() | |
fixer.addMissingAtoms() |
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-bash-4.1$ cat mpitest.o2365443 | |
3,2,1 | |
3,2,1 | |
3,2,1 | |
3,2,1 | |
gpu-1-4.local | |
gpu-1-4.local | |
gpu-1-4.local | |
gpu-1-5.local | |
grep: /var/spool/torque/aux/2365443.mskcc-fe1.localgpu: No such file or directory |
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import os | |
import mdtraj as md | |
import gzip | |
import tempfile | |
import glob | |
directories = glob.glob("./all_pdb/*") | |
for directory in directories: | |
filenames = glob.glob("%s/*.gz" % directory) | |
for filename in filenames: |
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import pandas as pd | |
import numpy as np | |
import pymbar | |
samples_per_state = 250 | |
n_states = 100 | |
rates = np.linspace(1, 3, n_states) | |
N_k = np.ones(n_states, 'int') * samples_per_state | |
n_samples = n_states * samples_per_state |
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import mdtraj as md | |
import numpy as np | |
def dipole_moment(traj, charges): | |
"""Compute the dipole moment of an MDTraj object.""" | |
xyz = md.compute_displacements(traj, np.array([[0, i] for i in range(traj.n_atoms)])).astype('float') | |
return xyz.transpose(0, 2, 1).dot(charges) |
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<?xml version="1.0" ?> | |
<State time="0" type="State" version="1"> | |
<PeriodicBoxVectors> | |
<A x="8.294880307685814" y="0" z="0" /> | |
<B x="0" y="8.294880307685814" z="0" /> | |
<C x="0" y="0" z="8.294880307685814" /> | |
</PeriodicBoxVectors> | |
<Parameters MonteCarloPressure="1.01325" /> | |
<Energies KineticEnergy="143998.28275239374" PotentialEnergy="23807.646244278643" /> | |
<Positions> |
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