Alternatives and similar repositories for pymbar-examples

Users that are interested in pymbar-examples are comparing it to the libraries listed below

• dspoel / remd-temperature-generator
  Temperature generator for Replica Exchange MD simulations
  ☆29Updated 2 years ago
• MikkelDA / COBY
  COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3
  ☆42Updated last week
• 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
  ☆38Updated 2 years ago
• leelasd / OPLS-AAM_for_Gromacs
  Gromacs Implementation of OPLS-AAM Force field
  ☆14Updated 7 years ago
• Inniag / openmm-scripts-amoeba
  OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field
  ☆27Updated 5 years ago
• drazen-petrov / SMArt
  ☆30Updated last week
• 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 6 years ago
• qusers / Q6
  Q6 Repository -- EVB, FEP and LIE simulator.
  ☆35Updated 2 years ago
• MobleyLab / SeparatedTopologies
  Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).
  ☆28Updated last year
• 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
• OpenBioSim / biosimspace_tutorials
  A tutorials suite for BioSimSpace.
  ☆31Updated last month
• UCL-CCS / TIES_MD
  Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.
  ☆33Updated last year
• pfizer-opensource / TorsionNet
  A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM
  ☆39Updated 2 years ago
• openmm / openmm_workshops
  ☆39Updated last year
• choderalab / espaloma-charge
  Standalone charge assignment from Espaloma framework.
  ☆44Updated last month
• rinikerlab / reeds
  This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…
  ☆32Updated 6 months ago
• emleddin / research-scripts
  Different run and analysis scripts as described in the research guides.
  ☆13Updated 3 years ago
• cbc-univie / transformato
  Set up relative free energy calculations using a common scaffold
  ☆24Updated 3 months ago
• essex-lab / grand
  A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.
  ☆72Updated 2 years ago
• arwalkerlab / AutoParams
  ☆28Updated last year
• openforcefield / ccpbiosim-2023
  Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week
  ☆31Updated 2 years ago
• DingGroup / BayesMBAR
  Bayesian Multistate Bennett Acceptance Ratio Method
  ☆15Updated last month
• harmsm / md-analysis-tools
  scripts for analyzing molecular dynamics trajectories using VMD
  ☆39Updated 10 years ago
• JingHuangLab / openmm_deepmd_plugin
  ☆22Updated 5 months ago
• MDAnalysis / UserGuide
  User Guide for MDAnalysis
  ☆29Updated this week
• fhh2626 / ABF-example-files-for-NAMD-and-OpenMM
  ☆10Updated 6 years ago
• rinikerlab / restraintmaker
  Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…
  ☆19Updated 3 years ago
• michellab / BioSimSpaceTutorials
  ☆25Updated last year
• jhenin / Methods-for-enhanced-sampling-and-free-energy-calculations
  Enhanced sampling methods for molecular dynamics simulations
  ☆41Updated 2 years ago
• gpantel / MD_methods-and-analysis
  Repository for MD methods and analysis from submitted or published work
  ☆19Updated 2 years ago