Alternatives and similar repositories for sDMD

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

• dspoel / remd-temperature-generator
  Temperature generator for Replica Exchange MD simulations
  ☆28Updated 2 years 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…
  ☆13Updated 4 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
• markusfleck / PARENT
  PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems
  ☆15Updated 3 years ago
• emleddin / research-scripts
  Different run and analysis scripts as described in the research guides.
  ☆13Updated 2 years ago
• dkoes / md-scripts
  A collections of scripts for working molecular dynamics simulations
  ☆43Updated last year
• ykhdrew / qMSM_tutorial
  A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison
  ☆16Updated 2 years ago
• federico-fogolari / pdb2entropy
  Entropy from PDB conformational ensembles
  ☆8Updated 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
  ☆34Updated last year
• OpenBioSim / biosimspace_tutorials
  A tutorials suite for BioSimSpace.
  ☆25Updated last month
• RagnarB83 / chemshell-QMMM-protein-setup
  MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…
  ☆23Updated 11 months ago
• choderalab / pymbar-examples
  Examples of applications of pymbar to various problems in simulation and experiment
  ☆21Updated 10 years ago
• JingHuangLab / openmm_deepmd_plugin
  ☆22Updated 2 weeks ago
• shirtsgroup / cg_openmm
  Tools to build coarse grained models and perform simulations with OpenMM
  ☆24Updated 2 years ago
• MikkelDA / COBY
  COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3
  ☆36Updated 2 weeks ago
• purnawanpp / plants
  Tutorial using PLANTS (Protein-Ligand ANTSystem)
  ☆10Updated 10 months ago
• HITS-MCM / tauRAMD
  Computation of the drug-target relative residence times from RAMD simulations
  ☆16Updated 9 months ago
• michellab / BioSimSpaceTutorials
  ☆25Updated last year
• sbhakat / AF-cryptic-pocket
  Cryptic pocket prediction using AlphaFold 2
  ☆22Updated 2 years ago
• 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
• Lemkul-Lab / gmx_tutorials_jpcb
  Input files for GROMACS tutorials written for the Journal of Physical Chemistry B
  ☆19Updated 10 months ago
• delemottelab / string-method-swarms-trajectories
  A python implementation of the string method with swarms of trajectories using GROMACS
  ☆18Updated 2 years ago
• LQCT / MDScan
  An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics
  ☆15Updated 2 years ago
• otayfuroglu / deepQM
  ☆28Updated last month
• JecaTosovic / WaterNetworkAnalysis
  Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis
  ☆17Updated 7 months ago
• ksy141 / mstool
  Multiscale Simulation Tool for Backmapping
  ☆17Updated 2 months ago
• DingGroup / BayesMBAR
  Bayesian Multistate Bennett Acceptance Ratio Method
  ☆13Updated 3 weeks ago
• HITS-MCM / gromacs-ramd
  Random Acceleration Molecular Dynamics in GROMACS
  ☆37Updated 10 months ago
• Gallicchio-Lab / openmm-atmmetaforce-plugin
  An OpenMM plugin that implements the Alchemical Transfer Potential
  ☆40Updated 2 years ago
• forlilab / waterkit
  Tool to predict water molecules placement and energy in ligand binding sites
  ☆28Updated last week