GitHub topics: namd
jfaraudo/Running_NAMD
Scripts useful for running NAMD simulations
Language: Rich Text Format - Size: 1.85 MB - Last synced at: about 22 hours ago - Pushed at: about 22 hours ago - Stars: 2 - Forks: 1
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.
Language: Python - Size: 375 KB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 3 - Forks: 3
Colvars/colvars
Collective variables library for molecular simulation and analysis programs
Language: C++ - Size: 42.4 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 219 - Forks: 58
Yuanming-Song/gmx2charmm
GROMACS to CHARMM Force Field File Converter
Language: Shell - Size: 371 KB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 0 - Forks: 0
Kitaolab/PaCS-Toolkit
PaCS-Toolkit: Optimized software utilities for PaCS-MD and following analysis
Language: Python - Size: 1.68 MB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 17 - Forks: 4
pedro-tulio/pyadmd
Setup and run aMDeNM simulations with Python
Language: Python - Size: 3.7 MB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 0 - Forks: 0
Marcello-Sega/pytim
a python package for the interfacial analysis of molecular simulations
Language: Python - Size: 206 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 85 - Forks: 35
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.
Language: Python - Size: 7.99 MB - Last synced at: 9 days ago - Pushed at: about 1 month ago - Stars: 17 - Forks: 3
MDAnalysis/imd-workshop-2024
Materials for the virtual 2024 MDAnalysis IMD streaming workshop.
Language: Jupyter Notebook - Size: 25.5 MB - Last synced at: 1 day ago - Pushed at: 4 months ago - Stars: 7 - Forks: 1
Adam-maz/Toolkit-for-NAMD
I present tools that accelerate molecular dynamics (MD) simulations using NAMD software and support the analysis of the obtained trajectories.
Language: Jupyter Notebook - Size: 29.2 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0
bio-phys/MDBenchmark
Quickly generate, start and analyze benchmarks for molecular dynamics simulations.
Language: Python - Size: 1.29 MB - Last synced at: 6 days ago - Pushed at: 8 months ago - Stars: 78 - Forks: 17
Molecular-Simulation-Lab-UV/NAMDAnalisisScripts
Scripts used for analysis of various systems and the pertaining variables or reaction coordinates
Language: Python - Size: 22.6 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 4
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)
Size: 12.7 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 6 - Forks: 1
JonathanHungerland/NAMD_AutoConf
Bash-based scripts to allow MD simulations with multiple stages using a single major configuration file.
Language: Tcl - Size: 15.9 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0
shmoe6/NAMD-Config-Generator
Config file generator for easier simulations with the Nanoscale Molecular Dynamics (NAMD) software.
Language: Python - Size: 1.85 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
gxf1212/md-highlighter
a VScode syntax highlight tool for molecular dynamics
Size: 3.67 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0
JasonWeinzierl/myoglobin
Term Paper for PHYS 4500 using NAMD and VMD to study the structure of myoglobin
Language: TeX - Size: 182 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
jhenin/SAFEP_tutorial
A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD
Language: TeX - Size: 676 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 1
cameronabrams/psfgen 📦
TcL/VMD/psfgen/bash scripts for generating MD systems for use with NAMD
Language: Tcl - Size: 10.2 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 9 - Forks: 4
m3g/ComplexMixtures.jl
Package to perform minimum-distance distribution analyses of complex solute-solvent interactions
Language: Julia - Size: 49.9 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 12 - Forks: 2
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.
Size: 7.28 MB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 31 - Forks: 7
Sarah-Hesham-2022/BioPhysics-Molecular-Dynamics-Simulation
Using VMD and NAMD for molecular dynamics simulation of protein PDB files.
Language: Tcl - Size: 57.3 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 2
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
Language: Python - Size: 32.9 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
HECBioSim/benchmark-suite
The HECBioSim benchmarking suite. Designed to be launched via Longbow to increase portability, thus benchmarks can be initiated on new machines with minimum effort. Useful for both users and system administrators.
Size: 1000 Bytes - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 0
cameronabrams/cfacv
A simple collective-variables module for NAMD via tclforces; implements TAMD
Language: C - Size: 9.27 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 4
spheex/pepdroidff_materials_studio
PEPDROID force field for peptoids
Language: Rich Text Format - Size: 36.1 KB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0
UCL-CCS/FabMD
FabMD is a FabSim3 plugin for automated LAMMPS-based simulations.
Language: Python - Size: 31.3 MB - Last synced at: 11 months ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 1
trishnasaha/3rd_PhD_Project_Virtual_Screening_Arginase_Inhibitor
Autodock-Vina, NAMD, VMD
Language: Perl - Size: 330 KB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0
jjti/tubulin-in-an-EEF
study of external electric fields' effects on the tubulin dimer via MD
Language: Tcl - Size: 12.5 MB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0
fhh2626/NAMD-xtb-QMMM-interface
NAMD-xtb-QMMM-interface
Language: Python - Size: 9.77 KB - Last synced at: about 2 years ago - Pushed at: almost 5 years ago - Stars: 8 - Forks: 5
francescopatane96/Molecular-dynamics-with-NAMD
Perform molecular dynamics experiments (MD) with NAMD on colab
Language: Jupyter Notebook - Size: 115 KB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
xh125/LVCSH-mpi
A Fortran code with MPI and Openmp to simulation the non-adiabatic Molecular Dynamics in the solid state Materials.
Language: Fortran - Size: 55.2 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0
radical-collaboration/MDFF-EnTK
MDFF-EnTK: Scalable Adaptive Protein Ensemble Refinement Integrating Flexible Fitting
Language: Slash - Size: 220 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 1
HITS-MBM/guides
Various guides about our tools
Size: 4.88 KB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0
