Alternatives and similar repositories for AMBER-Umbrella_COM_restraint_tutorial

Users that are interested in AMBER-Umbrella_COM_restraint_tutorial are comparing it to the libraries listed below

• 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
• Gallicchio-Lab / openmm-atmmetaforce-plugin
  An OpenMM plugin that implements the Alchemical Transfer Potential
  ☆39Updated 2 years ago
• IAlibay / MDRestraintsGenerator
  Python code for generating Boresch restraints from MD simulations
  ☆22Updated 2 months ago
• bigginlab / ABFE_workflow
  This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.
  ☆58Updated last week
• qusers / Q6
  Q6 Repository -- EVB, FEP and LIE simulator.
  ☆35Updated 2 years ago
• maxscheurer / pycontact
  Analysis of non-covalent interactions in MD trajectories
  ☆66Updated 11 months ago
• dspoel / remd-temperature-generator
  Temperature generator for Replica Exchange MD simulations
  ☆29Updated 3 years ago
• dkoes / md-scripts
  A collections of scripts for working molecular dynamics simulations
  ☆44Updated 4 months ago
• MDAnalysis / WorkshopMDMLEdinburgh2022
  ☆65Updated 5 months ago
• michellab / BioSimSpaceTutorials
  ☆25Updated last year
• choderalab / pymbar-examples
  Examples of applications of pymbar to various problems in simulation and experiment
  ☆23Updated 10 years ago
• limresgrp / FMAP_v1
  Codes to use funnel-metadynamics and funnel metadynamics automated protocol
  ☆30Updated 4 years ago
• 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
• pfizer-opensource / TorsionNet
  A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM
  ☆39Updated 2 years ago
• callumjd / AMBER-Membrane_protein_tutorial
  Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen
  ☆70Updated 2 years ago
• markusfleck / PARENT
  PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems
  ☆16Updated 3 years ago
• HITS-MCM / gromacs-ramd
  Random Acceleration Molecular Dynamics in GROMACS
  ☆42Updated last year
• openmm / openmm_workshops
  ☆40Updated last year
• ykhdrew / qMSM_tutorial
  A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison
  ☆18Updated 2 years 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
• GHeinzelmann / GHOAT.py
  The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.
  ☆21Updated 7 months ago
• essex-lab / grand
  A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.
  ☆72Updated 2 years ago
• cbc-univie / transformato
  Set up relative free energy calculations using a common scaffold
  ☆24Updated 4 months ago
• Gervasiolab / OpenBPMD
  ☆68Updated 2 years ago
• mms-fcul / PypKa
  A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism
  ☆63Updated last year
• UCL-CCS / TIES_MD
  Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.
  ☆34Updated 2 years ago
• drazen-petrov / SMArt
  ☆30Updated last week
• openforcefield / ptm_prototype
  ☆21Updated 2 weeks ago
• arwalkerlab / AutoParams
  ☆28Updated last year
• CCPBioSim / fesetup
  A tool for setting up free energy simulations.
  ☆36Updated 3 years ago