Collective variables library for molecular simulation and analysis programs
a python package for the interfacial analysis of molecular simulations
Quickly generate, start and analyze benchmarks for molecular dynamics simulations.
Database of hand-built OPLS-AA parameters and topologies for 464 molecules. Zip files contains parameter and topologies for OpenMM, Gromacs, NAMD, CHARMM, LAMMPS, TINKER, CNS/X-PLOR, Q, DESMOND, BOSS and MCPRO.
Longbow is a tool for automating simulations on a remote HPC machine. Longbow is designed to mimic the normal way an application is run locally but allows simulations to be sent to powerful machines.
PaCS-Toolkit: Optimized software utilities for PaCS-MD and following analysis
Package to perform minimum-distance distribution analyses of complex solute-solvent interactions
A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD
Using VMD and NAMD for molecular dynamics simulation of protein PDB files.
Tutorial for converting NAMD psf/pdb files to CHARMM PSF/CRD (credit attributed where appropriate to the AMAZING humans who developed these scripts)
All GROMACS/NAMD initializing files for generating initial structures for polydisperse chains with a set of residues desired by the user. With LigninBuilder, all lignin topologies can be built directly.
a VScode syntax highlight tool for molecular dynamics
Scripts useful for running NAMD simulations
study of external electric fields' effects on the tubulin dimer via MD
FabMD is a FabSim3 plugin for automated LAMMPS-based simulations.
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