Alternatives and similar repositories for ATRANET

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

• MikkelDA / COBY
  COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3
  ☆43Updated 2 months ago
• SimonBoothroyd / absolv
  Absolute solvation free energy calculations with OpenFF and OpenMM
  ☆26Updated last year
• dspoel / remd-temperature-generator
  Temperature generator for Replica Exchange MD simulations
  ☆29Updated 3 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.
  ☆24Updated 6 years ago
• choderalab / pymbar-examples
  Examples of applications of pymbar to various problems in simulation and experiment
  ☆23Updated 11 years ago
• Inniag / openmm-scripts-amoeba
  OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field
  ☆28Updated 5 years ago
• noegroup / reform
  A simple implementation of replica exchange MD simulations for OpenMM.
  ☆24Updated 4 years ago
• jhenin / Methods-for-enhanced-sampling-and-free-energy-calculations
  Enhanced sampling methods for molecular dynamics simulations
  ☆42Updated 3 years ago
• fjclark / red
  Robust Equilibration Detection
  ☆26Updated last week
• JingHuangLab / openmm_deepmd_plugin
  ☆24Updated 7 months ago
• openmm / openmm_workshops
  ☆44Updated last year
• TheJacksonLab / OpenMacromolecularGenome
  ☆21Updated 11 months ago
• JecaTosovic / WaterNetworkAnalysis
  Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis
  ☆18Updated this week
• NNairIITK / Enhanced_Sampling_Methods_Tutorials
  Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..
  ☆48Updated 5 years ago
• drazen-petrov / SMArt
  ☆31Updated 2 weeks ago
• IAlibay / MDRestraintsGenerator
  Python code for generating Boresch restraints from MD simulations
  ☆22Updated 4 months ago
• JecaTosovic / ConservedWaterSearch
  Python module for identification of conserved water molecules from molecular dynamics trajectories.
  ☆14Updated last week
• 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
• gpantel / MD_methods-and-analysis
  Repository for MD methods and analysis from submitted or published work
  ☆20Updated 2 years ago
• essex-lab / grand
  A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.
  ☆75Updated 2 years ago
• tonigi / vmd_extensions
  Convenience functions for VMD-TCL scripting
  ☆14Updated 6 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
• Abdelazim-Abdelgawwad / easyPARM
  easyPARM is a computational tool developed to simplify the derivation of force field parameters for metal-containing molecular systems an…
  ☆32Updated 2 weeks ago
• OpenBioSim / biosimspace_tutorials
  A tutorials suite for BioSimSpace.
  ☆34Updated 3 months ago
• duartegroup / metallicious
  ☆19Updated last month
• federico-fogolari / pdb2entropy
  Entropy from PDB conformational ensembles
  ☆13Updated last year
• 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 8 months ago
• markusfleck / PARENT
  PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems
  ☆16Updated 4 years ago
• mme-ucl / MFI
  ☆13Updated 6 months ago
• emleddin / research-scripts
  Different run and analysis scripts as described in the research guides.
  ☆13Updated 3 years ago