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autodock-gpu

AutoDock for GPUs using OpenCL

colvars

Collective variables module for molecular simulation and analysis programs

deltavina

DeltaVina scoring function

fastmerge

Tool for quickly merging together molecules saved as .js files made in VMD.

files_lignin

All GROMACS initializing files for lignin structures in poplar/switchgrass

griddataformats

GridDataFormats is a pure Python library to handle data on a regular grid using commonly used file formats in molecular simulations.

hmmmsolvents

Companion to the SCSE and SCSM solvent paper, with code to make it easier to use!

latexcodec

Lexer and codec to work with LaTeX code in Python.

lignin-kmc

ligninbuilder

VMD Plugin and associated scripts to build lignin structures from topological specifications

ligningraphs

Lignin Structure Determination with Multiscale Graph Modeling

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

parmed

Parameter/topology editor and molecular simulator

pbctools

Note that the pbctools are not developed in this repository anymore, but in the main VMD code.

pchem-purdue.github.io

pynamd

Python Tools for NAMD

software-building-instructions

Instructions for Building Software on Various Platforms

solventboxgeneration

Scripts and tools to generate solvent boxes suitable for use with the VMD solvate plugin

topotools

VMD plugin for manipulating topology information

turkeyrun

vecexpr

Vector-based pocket calculator for Tcl.

vmd-packaging-instructions

Instructions for how to package VMD for Ubuntu and not pull your hair out in the process.

vmd-python

Installable VMD as a python module

vmd-tprreader

Molfileplugin for VMD that lets me read in GROMACS tpr files

zerotemperaturestring

Python Implementation of the zero temperature string method