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.
PaCS-Toolkit: Optimized software utilities for PaCS-MD and following analysis
Package to perform minimum-distance distribution analyses of complex solute-solvent interactions
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.
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.
xBFreE is a powerful and versatile tool for computing the Binding Free Energies using a variety of methods across popular Molecular Dynamics programs
Scripts useful for running NAMD simulations
a VScode syntax highlight tool for molecular dynamics
Reproduction data for paper "Spin Valley Dynamics Entangled with Optical Fields, Phonons, and Spin-Orbit Coupling in Monolayer MoSe2" at https://onlinelibrary.wiley.com/doi/10.1002/adom.202403069
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