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carlsim3

CARLsim is an efficient, easy-to-use, GPU-accelerated software framework for simulating large-scale spiking neural network (SNN) models with a high degree of biological detail.

cassandra

Cassandra is a Monte Carlo package to conduct atomistic simulations.

cbe60499

Nonlinear and Stochastic Optimization. https://ndcbe.github.io/CBE60499/

constrainmol

Simple bond constraint solver

foyer

A package for atom-typing as well as applying and disseminating forcefields

gaff-foyer

gmso

Flexible storage of chemical topology for molecular simulation

kh_screening

libgmxfort

Modern Fortran toolkit for analyzing GROMACS simulations

libxdrfile

Fork of library used in reading xtc files from GROMACS simulations

mbuild

A hierarchical, component based molecule builder

mbuild-cookiecutter

Cookiecutter for mBuild recipes

mdtraj

An open library for the analysis of molecular dynamics trajectories

miktex

the MiKTeX source code

ml_molsim2020

Machine learning exercises for the MolSim course (http://www.acmm.nl/molsim/molsim2020/index.html)

mosdef_cassandra

MoSDeF compatible wrapper for Cassandra Monte Carlo code

ops_tutorial

Introductory tutorial on TPS, committor analysis, and (MS)TIS with OpenPathSampling

planetsdracula

My plan to leave Earth

rdk

Random Dot Kinetogram (RDK) - R. Gilmore

reproducibility_study

Repo for data collection, discussion, etc for a MoSDeF reproducibility study.

xyz2mol

Converts an xyz file to an RDKit mol object