kyleabeauchamp

kyleabeauchamp

<?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>

kyleabeauchamp

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)

kyleabeauchamp

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

kyleabeauchamp

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:

kyleabeauchamp

-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

kyleabeauchamp

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()

kyleabeauchamp

#!/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

kyleabeauchamp

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()

kyleabeauchamp

from msmbuilder import io
from msmbuilder import MSMLib

ass = io.loadh("~/dat/redesign/NTL9/Ward-2500/Assignments.Fixed.h5")["Data"]
c = MSMLib.get_count_matrix_from_assignments(ass)
m = MSMLib.reversible_MLE_estimator(c)
u = m.optimize()
c0 = c + c.transpose()
c.data[:] = 1.
c3 = MSMLib.mle_reversible_count_matrix(c,initial_guess=c0)