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adaptivemd

A python framework to run adaptive Markov state model (MSM) simulation on HPC resources

adaptivesampling

amberutils

Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods

async_re-openmm

Asynchronous Replica Exchange Framework for Heterogeneous Computing by using OpenMM engine

autorungamess

auto RUN a lot of GAMESS jobs

awesome-cheminformatics

A curated list of Cheminformatics libraries and software.

caddhom

For CADD or Computational Biology Project

calc-ir-spectra-from-lammps

This code shows how to calculate an IR spectrum from a LAMMPS MD simulation.

cellgrid

checkensemble

This software allows users to perform statistical test to determine if a given molecular simulation is consistent with the thermodynamic ensemble it is performed in.

complex_tool

Extract monomer and contact info from complex PDB file

coordgenlibs

Schrodinger-developed 2D Coordinate Generation

covid

MolSSI SARS-CoV-2 Biomolecular Simulation Data and Algorithm Store

createremddirs

Automatically generate input for running M-REMD simulations (and more) in Amber.

dabble

Membrane protein builder and parameterizer

deepalign

DeepAlign: the protein structure analysis toolkit

demystifying

dtnn

Deep Tensor Neural Network

egfp-scripts

epithelial

model of a complex epithelial cell membrane

freesolv

Experimental and calculated small molecule hydration free energies

frontier-expansion-sampling

gcc_five_minute

gcc五分钟系列

getcontacts

Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation

github-issues-blog

基于 Github issues 的单页面静态博客

gitpresentation

Presentation material for MD lab git tutorial

gmx_protocols

Protocols for running MD simulations in Gromacs

gmx_template

This is a template/example of MD simulations using Gromacs

gmxtool

tools for GROMACS

gpcr-string-method-2019