Alternatives and similar repositories for pDynamo3

Users that are interested in pDynamo3 are comparing it to the libraries listed below

• cdsgroup / resp
  A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4
  ☆34Updated 6 months ago
• openmm / openmm-plumed
  OpenMM plugin to interface with PLUMED
  ☆73Updated 2 months ago
• MDAnalysis / WorkshopMDMLEdinburgh2022
  ☆65Updated 5 months ago
• bioexcel / gromacs-2022-cp2k-tutorial
  Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface
  ☆41Updated 4 years ago
• qusers / Q6
  Q6 Repository -- EVB, FEP and LIE simulator.
  ☆35Updated 2 years ago
• Martini-Force-Field-Initiative / M3-Small-Molecules
  Martini 3 small molecule database
  ☆68Updated 3 months ago
• openmm / openmm_workshops
  ☆40Updated last year
• dspoel / remd-temperature-generator
  Temperature generator for Replica Exchange MD simulations
  ☆29Updated 3 years ago
• mms-fcul / PypKa
  A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism
  ☆65Updated last year
• JingHuangLab / openmm_deepmd_plugin
  ☆22Updated 6 months ago
• lilyminium / psiresp
  RESP with inter- and intra-molecular constraints in Psi4.
  ☆32Updated 2 years ago
• MikkelDA / COBY
  COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3
  ☆42Updated last month
• Gallicchio-Lab / openmm-atmmetaforce-plugin
  An OpenMM plugin that implements the Alchemical Transfer Potential
  ☆39Updated 2 years ago
• openforcefield / openff-bespokefit
  Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.
  ☆71Updated this week
• maccallumlab / martini_openmm
  ☆61Updated last month
• CCPBioSim / qmmm-workshop
  A repository containing the build steps for the ccpbiosim workshop on QM/MM
  ☆68Updated 2 weeks ago
• NNairIITK / Enhanced_Sampling_Methods_Tutorials
  Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..
  ☆49Updated 4 years ago
• alchemistry / alchemical-best-practices
  Best practice document for alchemical free energy calculations going to livecoms journal
  ☆81Updated 2 weeks ago
• maxscheurer / pycontact
  Analysis of non-covalent interactions in MD trajectories
  ☆65Updated last year
• essex-lab / grand
  A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.
  ☆74Updated 2 years ago
• MiaoLab20 / gamd-openmm
  Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…
  ☆89Updated 5 months ago
• choderalab / pymbar-examples
  Examples of applications of pymbar to various problems in simulation and experiment
  ☆24Updated 10 years ago
• YAMACS-SML / YAMACS
  Yasara plugins for Gromacs users
  ☆32Updated 2 years ago
• choderalab / espaloma-charge
  Standalone charge assignment from Espaloma framework.
  ☆46Updated 3 months ago
• callumjd / AMBER-Umbrella_COM_restraint_tutorial
  Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane
  ☆39Updated 2 years ago
• RagnarB83 / chemshell-QMMM-protein-setup
  MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…
  ☆24Updated last year
• mobiochem / MoBioTools
  A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…
  ☆30Updated last year
• grimme-lab / crest
  Conformer-Rotamer Ensemble Sampling Tool based on the xtb Semiempirical Extended Tight-Binding Program Package
  ☆34Updated last month
• cbc-univie / transformato
  Set up relative free energy calculations using a common scaffold
  ☆24Updated 4 months ago
• BrooksResearchGroup-UM / pyCHARMM-Workshop
  pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…
  ☆72Updated last week