namd

There are 1 repository under namd topic.

• Colvars / colvars

  Collective variables library for molecular simulation and analysis programs

  collective-variablesenhanced-samplingfree-energygromacslammpsmolecular-dynamicsnamdsimulationtinkerhpvmd
  Language:C++ 190

• Marcello-Sega / pytim

  a python package for the interfacial analysis of molecular simulations

  simulationsmolecular-dynamicsdata-analysismdanalysisgromacsnamdcharmmlammpsinterfacesscientific-computingwillard-chandlermolecular-simulationsmdtrajinterfacial-atomsopenmmpythonsasa
  Language:Python 76

• bio-phys / MDBenchmark

  Quickly generate, start and analyze benchmarks for molecular dynamics simulations.

  benchmarkclicomputational-chemistrygromacshigh-performance-computingmolecular-dynamicsnamdpythonsimulation
  Language:Python 72

• 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.

  molecular-dynamicsmolecular-simulationforce-fieldopls-aalammpsgromacsnamdcharmmtinkeropenmmthermodynamics
  31

• 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.

  amberautomationbioinformaticsbiosimulationcharmmgromacshigh-performance-computingjob-queuejob-schedulerjob-submissionlammpslsf-jobsmolecular-dynamicsnamdpbs-proscientific-computingsgeslurmsupercomputertorque
  Language:Python 17

• m3g / ComplexMixtures.jl

  Package to perform minimum-distance distribution analyses of complex solute-solvent interactions

  amberchemistrydistribution-functiongromacslammpsmolecular-dynamicsmolecular-dynamics-simulationmolecular-modelingmolecular-simulationnamd
  Language:Julia 14

• fhh2626 / NAMD-xtb-QMMM-interface

  NAMD-xtb-QMMM-interface

  namdqmmm
  Language:Python 10

• cameronabrams / psfgen

  TcL/VMD/psfgen/bash scripts for generating MD systems for use with NAMD

  charmmtclpdbpsfgenvmdnamdbashpythoncswig
  Language:Tcl 9

• jhenin / SAFEP_tutorial

  A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD

  safepalchemyfree-energy-calculationsnamdtutorial
  Language:TeX 8

• Sarah-Hesham-2022 / BioPhysics-Molecular-Dynamics-Simulation

  Using VMD and NAMD for molecular dynamics simulation of protein PDB files.

  bioinformaticsbiophysicsmolecular-dynamics-simulationnamdpdb-filesproblem-solvingprogrammingproteinsstructural-bioinformaticsstructural-biologytcl-tktrajectoryvisulaizationvmdnanoscale-molecular-dynamicsvisualization-molecular-dynamicsforce-filedwaterbox
  Language:Tcl 5

• cameronabrams / cfacv

  A simple collective-variables module for NAMD via tclforces; implements TAMD

  namdtcl
  Language:C 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)

  namdmolecular-dynamicscharmmcharmm-gui
  4

• Kitaolab / PaCS-Toolkit

  PaCS-Toolkit: Optimized software utilities for PaCS-MD and following analysis

  amberfugakugromacshpcimsisspmolecular-dynamicsnamdproteinsimulationtsubame
  Language:Python 4

• 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.

  gromacswrappernamdligninbuilder
  Language:Python 3

• Biu-G / gromacs-rocm

  Gromacs that can be accelerated at AMD GPU

  gromacsamdgpuhiprocmhipifynamdamber
  Language:C++ 2

• jfaraudo / Running_NAMD

  Scripts useful for running NAMD simulations

  moleculardynamicsnamdsimulation
  Language:Rich Text Format 2

• jjti / tubulin-in-an-EEF

  study of external electric fields' effects on the tubulin dimer via MD

  namdresearchsimulation
  Language:Tcl 1

• Molecular-Simulation-Lab-UV / NAMDAnalisisScripts

  Scripts used for analysis of various systems and the pertaining variables or reaction coordinates

  analysisnamdpythontcltrajectories
  Language:Python 1

• UCL-CCS / FabMD

  FabMD is a FabSim3 plugin for automated LAMMPS-based simulations.

  multiscale-simulationpython3high-performance-computinglammpsnamdgromacs
  Language:Python 1

• francescopatane96 / Molecular-dynamics-with-NAMD

  Perform molecular dynamics experiments (MD) with NAMD on colab

  bioinformaticsbiotechnologydynamicsmoleculardynamicssimulationcharmmisoformsmdminimizationmolecular-dynamicsmutantsnamdpdbproteindynamicssimulationequilibrationgroomacs
  Language:Jupyter Notebook 0

• gxf1212 / md-highlighter

  a VScode syntax highlight tool for molecular dynamics

  gromacsmol2molecular-dynamics-simulationmolecular-modelingmolecular-simulationnamdpsfrtfsdf
  0

• HITS-MBM / guides

  Various guides about our tools

  gromacsnamdfda
  0

• JasonWeinzierl / myoglobin

  Term Paper for PHYS 4500 using NAMD and VMD to study the structure of myoglobin

  physicsvmdnamd
  Language:TeX 0

• SolomonHaw / 50000025_NAMD_HPCAI

  NAMD build guideline for submission to APAC HPC-AI Competition 2020. Built and tested on the NSCC ASPIRE 1 supercomputer.

  hpcainamdcharm
  0
• pepdroidff_materials_studio

  spheex / pepdroidff_materials_studio

  PEPDROID force field for peptoids

  peptoidforcefieldmaterialsstudioforcefieldnamdcharmmpdbmol2dreiding
  Language:Rich Text Format 0

• trishnasaha / 3rd_PhD_Project_Virtual_Screening_Arginase_Inhibitor

  Autodock-Vina, NAMD, VMD

  autodock-vinanamdperlshell-scripttclvmd
  Language:Perl 0

• 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

  amberambertoolscharmmenergy-calculationsgmx-mmgbsagmx-mmpbsagromacsmd-simulationsmmgbsammpbsanamd
  Language:Python 0

• JonathanHungerland / NAMD_AutoConf

  Bash-based scripts to allow MD simulations with multiple stages using a single major configuration file.

  biophysicsmolecular-dynamicsnamd
  Language:Tcl

• radical-collaboration / MDFF-EnTK

  MDFF-EnTK: Scalable Adaptive Protein Ensemble Refinement Integrating Flexible Fitting

  namdsummitentkworkflow-engine
  Language:Slash

• shmoe6 / NAMD-Config-Generator

  Config file generator for easier simulations with the Nanoscale Molecular Dynamics (NAMD) software.

  namdvmdpython3guimolecular-dynamics
  Language:Python

• xh125 / LVCSH-mpi

  A Fortran code with MPI and Openmp to simulation the non-adiabatic Molecular Dynamics in the solid state Materials.

  fsshnamd
  Language:Fortran