Alternatives and similar repositories for masterclass-plumed:

Users that are interested in masterclass-plumed are comparing it to the libraries listed below

• IAlibay / MDRestraintsGenerator
  Python code for generating Boresch restraints from MD simulations
  ☆20Updated 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
• shirtsgroup / cg_openmm
  Tools to build coarse grained models and perform simulations with OpenMM
  ☆22Updated 2 years ago
• dspoel / remd-temperature-generator
  Temperature generator for Replica Exchange MD simulations
  ☆28Updated 2 years ago
• openmm / openmm_workshops
  ☆33Updated 7 months ago
• MottaStefano / PathDetect-SOM
  A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)
  ☆10Updated 3 years ago
• michellab / BioSimSpaceTutorials
  ☆25Updated last year
• UCL-CCS / TIES_MD
  Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.
  ☆32Updated last year
• forlilab / waterkit
  Tool to predict water molecules placement and energy in ligand binding sites
  ☆28Updated last week
• OpenBioSim / biosimspace_tutorials
  A tutorials suite for BioSimSpace.
  ☆24Updated last week
• chonglab-pitt / wedap
  Weighted Ensemble Data Analysis and Plotting
  ☆23Updated 7 months ago
• ykhdrew / qMSM_tutorial
  A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison
  ☆15Updated last year
• HITS-MCM / gromacs-ramd
  Random Acceleration Molecular Dynamics in GROMACS
  ☆36Updated 8 months ago
• visvaldask / gmx_makecyclictop
  This script makes a cyclic peptide or cyclic nucleotide topology file for GROMACS out of (specially prepared) linear molecule topology fi…
  ☆12Updated 4 years ago
• otayfuroglu / deepQM
  ☆27Updated 10 months ago
• openforcefield / ccpbiosim-2023
  Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week
  ☆30Updated 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…
  ☆31Updated 2 weeks ago
• Gallicchio-Lab / openmm-atmmetaforce-plugin
  An OpenMM plugin that implements the Alchemical Transfer Potential
  ☆40Updated last year
• 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
  ☆31Updated last year
• emleddin / research-scripts
  Different run and analysis scripts as described in the research guides.
  ☆13Updated 2 years ago
• mqcomplab / PRIME
  protein structure prediction with precision
  ☆17Updated 11 months ago
• cbc-univie / transformato
  Set up relative free energy calculations using a common scaffold
  ☆22Updated last week
• dkoes / md-scripts
  A collections of scripts for working molecular dynamics simulations
  ☆43Updated 10 months ago
• dlukauskis / funnel_maker
  Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.
  ☆13Updated last year
• BartBruininks / mdvwhole
  Density based object completion over PBC.
  ☆29Updated 4 months ago
• JecaTosovic / WaterNetworkAnalysis
  Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis
  ☆17Updated 5 months ago
• sbhakat / AF-cryptic-pocket
  Cryptic pocket prediction using AlphaFold 2
  ☆22Updated 2 years ago
• DingGroup / BayesMBAR
  Bayesian Multistate Bennett Acceptance Ratio Method
  ☆13Updated 3 months ago
• drazen-petrov / SMArt
  ☆26Updated 3 weeks ago
• seekrcentral / seekr2
  Simulation-Enabled Estimation of Kinetic Rates - Version 2
  ☆28Updated last month