Josh Vermaas's repositories
LigninBuilder
VMD Plugin and associated scripts to build lignin structures from topological specifications
Software-Building-Instructions
Instructions for Building Software on Various Platforms
vmd-tprreader
Molfileplugin for VMD that lets me read in GROMACS tpr files
vmd-packaging-instructions
Instructions for how to package VMD for Ubuntu and not pull your hair out in the process.
zerotemperaturestring
Python Implementation of the zero temperature string method
AutoDock-GPU
AutoDock for GPUs using OpenCL
deltavina
DeltaVina scoring function
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.
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.
pynamd
Python Tools for NAMD
solventboxgeneration
Scripts and tools to generate solvent boxes suitable for use with the VMD solvate plugin
topotools
VMD plugin for manipulating topology information
vmd-python
Installable VMD as a python module