namd
There are 30 repositories under namd topic.
Colvars/colvars
Collective variables library for molecular simulation and analysis programs
Marcello-Sega/pytim
a python package for the interfacial analysis of molecular simulations
bio-phys/MDBenchmark
Quickly generate, start and analyze benchmarks for molecular dynamics simulations.
leelasd/OPLSAA-DB
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.
HECBioSim/Longbow
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.
m3g/ComplexMixtures.jl
Package to perform minimum-distance distribution analyses of complex solute-solvent interactions
Kitaolab/PaCS-Toolkit
PaCS-Toolkit: Optimized software utilities for PaCS-MD and following analysis
fhh2626/NAMD-xtb-QMMM-interface
NAMD-xtb-QMMM-interface
cameronabrams/psfgen
TcL/VMD/psfgen/bash scripts for generating MD systems for use with NAMD
jhenin/SAFEP_tutorial
A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD
Sarah-Hesham-2022/BioPhysics-Molecular-Dynamics-Simulation
Using VMD and NAMD for molecular dynamics simulation of protein PDB files.
fearlessroad/NAMD_to_CHARMM-GUI
Tutorial for converting NAMD psf/pdb files to CHARMM PSF/CRD (credit attributed where appropriate to the AMAZING humans who developed these scripts)
cameronabrams/cfacv
A simple collective-variables module for NAMD via tclforces; implements TAMD
vaidyanathanms/SPRInG_PolydispersePolymerBuilder
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.
Biu-G/gromacs-rocm
Gromacs that can be accelerated at AMD GPU
gxf1212/md-highlighter
a VScode syntax highlight tool for molecular dynamics
jfaraudo/Running_NAMD
Scripts useful for running NAMD simulations
jjti/tubulin-in-an-EEF
study of external electric fields' effects on the tubulin dimer via MD
Molecular-Simulation-Lab-UV/NAMDAnalisisScripts
Scripts used for analysis of various systems and the pertaining variables or reaction coordinates
UCL-CCS/FabMD
FabMD is a FabSim3 plugin for automated LAMMPS-based simulations.
francescopatane96/Molecular-dynamics-with-NAMD
Perform molecular dynamics experiments (MD) with NAMD on colab
HITS-MBM/guides
Various guides about our tools
JasonWeinzierl/myoglobin
Term Paper for PHYS 4500 using NAMD and VMD to study the structure of myoglobin
JonathanHungerland/NAMD_AutoConf
Bash-based scripts to allow MD simulations with multiple stages using a single major configuration file.
shmoe6/NAMD-Config-Generator
Config file generator for easier simulations with the Nanoscale Molecular Dynamics (NAMD) software.
spheex/pepdroidff_materials_studio
PEPDROID force field for peptoids
trishnasaha/3rd_PhD_Project_Virtual_Screening_Arginase_Inhibitor
Autodock-Vina, NAMD, VMD
xBFreEnergy/xBFreE
xBFreE is a powerful and versatile tool for computing the Binding Free Energies using a variety of methods across popular Molecular Dynamics programs
radical-collaboration/MDFF-EnTK
MDFF-EnTK: Scalable Adaptive Protein Ensemble Refinement Integrating Flexible Fitting
xh125/LVCSH-mpi
A Fortran code with MPI and Openmp to simulation the non-adiabatic Molecular Dynamics in the solid state Materials.