moldyn / dcTMD

Related projects ⓘ

Alternatives and complementary repositories for dcTMD

• luigibonati / masterclass-plumed
  ☆10Updated 5 months ago
• federico-fogolari / pdb2entropy
  Entropy from PDB conformational ensembles
  ☆7Updated 7 months ago
• ykhdrew / qMSM_tutorial
  A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison
  ☆14Updated last year
• shirtsgroup / cg_openmm
  Tools to build coarse grained models and perform simulations with OpenMM
  ☆20Updated last year
• OpenBioSim / biosimspace_tutorials
  A tutorials suite for BioSimSpace.
  ☆16Updated this week
• fmaschietto / mdigest
  ☆29Updated last month
• ksy141 / mstool
  Multiscale Simulation Tool for Backmapping
  ☆16Updated this week
• LQCT / MDScan
  An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics
  ☆15Updated 2 years ago
• DingGroup / BayesMBAR
  Bayesian Multistate Bennett Acceptance Ratio Method
  ☆12Updated 3 weeks ago
• noegroup / reform
  A simple implementation of replica exchange MD simulations for OpenMM.
  ☆22Updated 3 years ago
• drazen-petrov / SMArt
  ☆26Updated last month
• mme-ucl / MFI
  ☆12Updated last month
• martimunicoy / peleffy
  The peleffy (PELE Force Field Yielder) is a Python package that builds PELE-compatible force field templates.
  ☆12Updated 3 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
• cbc-univie / transformato
  Set up relative free energy calculations using a common scaffold
  ☆22Updated 3 months ago
• MobleyLab / SeparatedTopologies
  Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).
  ☆22Updated this week
• JecaTosovic / WaterNetworkAnalysis
  Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis
  ☆15Updated 3 weeks ago
• sbhakat / AF-cryptic-pocket
  Cryptic pocket prediction using AlphaFold 2
  ☆22Updated 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…
  ☆30Updated 9 months ago
• chonglab-pitt / wedap
  Weighted Ensemble Data Analysis and Plotting
  ☆19Updated 2 months ago
• MiaoLab20 / pyreweighting
  ☆25Updated last year
• KULL-Centre / DEERpredict
  Software for the prediction of DEER and PRE data from conformational ensembles.
  ☆12Updated 2 months ago
• openmm / openmm_workshops
  ☆32Updated 2 months ago
• Multiscale-Modelling-of-Complex-Systems / 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…
  ☆15Updated 4 months ago
• MauriceKarrenbrock / HPC_Drug
  A middleware python tool for computational drug discovery on HPC architectures
  ☆9Updated 9 months ago
• UCL-CCS / TIES_MD
  Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.
  ☆32Updated 11 months ago
• JoaoRodrigues / openmm_scripts
  Collection of Python scripts to setup and run simulations with OpenMM
  ☆14Updated 4 years ago
• IAlibay / MDRestraintsGenerator
  Python code for generating Boresch restraints from MD simulations
  ☆18Updated 2 years ago
• Gallicchio-Lab / openmm-atmmetaforce-plugin
  An OpenMM plugin that implements the Alchemical Transfer Potential
  ☆37Updated last year
• michellab / BioSimSpaceTutorials
  ☆25Updated 10 months ago