dwhswenson

Wigner:~/Downloads/tmp dwhs$ ipython nbconvert Alanine\ Example.ipynb
[NbConvertApp] Using existing profile dir: u'/Users/dwhs/.ipython/profile_default'
[NbConvertApp] Converting notebook Alanine Example.ipynb to html
[NbConvertApp] Support files will be in Alanine Example_files/
Traceback (most recent call last):
  File "/opt/local/bin/ipython", line 5, in <module>
    start_ipython()
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/IPython/__init__.py", line 120, in start_ipython
    return launch_new_instance(argv=argv, **kwargs)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/IPython/config/application.py", line 564, in launch_instance

dwhswenson

dwhswenson

Optimization of the SequentialEnsemble

This gist includes files I used to look into performance questions for the SequentialEnsemble in OpenPathSampling.

This gist is to attach some files which relate to the discussion in OPS #222.

dwhswenson

dwhswenson

dwhswenson

dwhswenson

dwhswenson

dwhswenson

Alanine dipeptide committor stuff

This directory is part of a collaboration with Max Welling and his colleagues Rianne van den Berg and Thomas Kipf. We're playing with ways to use deep learning neural networks in the context of chemistry.

This is mainly for me to create some useful data for them, and for me to explain some of the tools that I think they will find useful. Some of this may get re-purposed into OpenPathSampling examples.

dwhswenson

#!/usr/bin/env python
# coding: utf-8

##########################################################################
# this script was generated by openmm-builder. to customize it further,
# you can save the file to disk and edit it with your favorite editor.
##########################################################################

# REQUIRES:
# * OpenMM (core dynamics)