Alternatives and similar repositories for MDRefine

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

• pablo-arantes / ParametrizANI
  Free Parametrization for Small Molecules
  ☆36Updated this week
• BILAB / pdb2oniom
  A python implementation of pdb2oniom for QM/MM (ONIOM) calculations
  ☆10Updated last year
• shirtsgroup / cg_openmm
  Tools to build coarse grained models and perform simulations with OpenMM
  ☆24Updated 2 years ago
• bioexcel / cp2K_qmmm_tutorials_for_biological_simulations
  Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.
  ☆22Updated 5 years ago
• MikkelDA / COBY
  COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3
  ☆40Updated last week
• samplchallenges / SAMPL9
  ☆30Updated last year
• choderalab / espaloma-charge
  Standalone charge assignment from Espaloma framework.
  ☆40Updated last year
• openmm / openmm_workshops
  ☆38Updated 11 months ago
• Honza-R / PL-REX
  Data set of protein-ligand complexes with reliable experimental structures and affinities
  ☆37Updated 6 months ago
• ksy141 / mstool
  Multiscale Simulation Tool for Backmapping
  ☆18Updated 2 weeks ago
• forlilab / waterkit
  Tool to predict water molecules placement and energy in ligand binding sites
  ☆28Updated last week
• openforcefield / openff-sage
  Scripts, inputs and the results generated as part of the training the Sage line of OpenFF force fields.
  ☆21Updated 2 months ago
• GoMartini3-tools / Native-contacts-determination-from-MD
  We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…
  ☆16Updated last year
• MiaoLab20 / pyreweighting
  ☆28Updated last year
• JecaTosovic / ConservedWaterSearch
  Python module for identification of conserved water molecules from molecular dynamics trajectories.
  ☆12Updated last month
• chonglab-pitt / wedap
  Weighted Ensemble Data Analysis and Plotting
  ☆24Updated 2 months ago
• smu-tao-group / LAST
  LAST: Latent Space Assisted Adaptive Sampling for Protein Trajectories
  ☆12Updated 2 years ago
• Abdelazim-Abdelgawwad / easyPARM
  easyPARM is a computational tool developed to simplify the derivation of force field parameters for metal-containing molecular systems an…
  ☆25Updated last month
• Acellera / quantumbind_rbfe
  Input files and binding free energy values from our benchmark with QuantumBind-RBFE
  ☆14Updated 4 months ago
• dspoel / remd-temperature-generator
  Temperature generator for Replica Exchange MD simulations
  ☆29Updated 2 years ago
• choderalab / kinase-metadynamics
  To run metadynamics simulations using openMM (based on Peter Eastman's script)
  ☆13Updated 6 years ago
• pfizer-opensource / TorsionNet
  A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM
  ☆39Updated 2 years ago
• KMNitesh05 / GROMACS_tutorial
  ☆40Updated 2 years ago
• HITS-MCM / gromacs-ramd
  Random Acceleration Molecular Dynamics in GROMACS
  ☆39Updated last year
• tiwarylab / af2rave
  Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2
  ☆57Updated 3 weeks ago
• JecaTosovic / WaterNetworkAnalysis
  Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis
  ☆17Updated last month
• ci-lab-cz / crem-dock
  CReM-dock: generation of chemically reasonable molecules guided by molecular docking
  ☆26Updated this week
• OpenBioSim / biosimspace_tutorials
  A tutorials suite for BioSimSpace.
  ☆25Updated 3 months ago
• dkoes / md-scripts
  A collections of scripts for working molecular dynamics simulations
  ☆44Updated 3 weeks ago
• rinikerlab / restraintmaker
  Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…
  ☆19Updated 2 years ago