Ivy Zhang zhang-ivy

## 9_debug_long_correction_slowdown.ipynb

      
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                zhang-ivy
                / 9_debug_long_correction_slowdown.ipynb
            
            
              Created
              December 8, 2021 17:07
            
              
                long range correction experiments
              
          
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## analysis_notebook_example.ipynb

      
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                / analysis_notebook_example.ipynb
            
            
              Created
              November 15, 2021 21:41
            
          
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## test_peters_long_range_speedup.ipynb

      
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                zhang-ivy
                / test_peters_long_range_speedup.ipynb
            
            
              Created
              September 22, 2021 14:55
            
          
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## example_for_kevin.ipynb

      
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                zhang-ivy
                / example_for_kevin.ipynb
            
            
              Created
              September 2, 2021 20:57
            
              
                OpenMM examples
              
          
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## amber.xml
<?xml version="1.0" ?>
<System openmmVersion="7.5" type="System" version="1">
	<PeriodicBoxVectors>
		<A x="2" y="0" z="0"/>
		<B x="0" y="2" z="0"/>
		<C x="0" y="0" z="2"/>
	</PeriodicBoxVectors>
	<Particles>
		<Particle mass="1.008"/>
		<Particle mass="12.01"/>

## run_neq_distrib.py
import logging
import pickle
import numpy as np
from openmmtools.integrators import PeriodicNonequilibriumIntegrator
from simtk import unit
from simtk import openmm
import argparse
import os
import time
import mdtraj as md

## prep_ncmc_movie.ipynb

      
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                zhang-ivy
                / prep_ncmc_movie.ipynb
            
            
              Last active
              August 6, 2020 17:12
            
              
                prep_ncmc_movie
              
          
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## fitting_kds.ipynb

      
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                zhang-ivy
                / fitting_kds.ipynb
            
            
              Last active
              June 22, 2020 19:50
            
              
                From Joe Cunningham
              
          
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	<?xml version="1.0" ?>
	<System openmmVersion="7.5" type="System" version="1">
	<PeriodicBoxVectors>
	<A x="2" y="0" z="0"/>
	<B x="0" y="2" z="0"/>
	<C x="0" y="0" z="2"/>
	</PeriodicBoxVectors>
	<Particles>
	<Particle mass="1.008"/>
	<Particle mass="12.01"/>
	import logging
	import pickle
	import numpy as np
	from openmmtools.integrators import PeriodicNonequilibriumIntegrator
	from simtk import unit
	from simtk import openmm
	import argparse
	import os
	import time
	import mdtraj as md