harmsm / md-analysis-toolsLinks
scripts for analyzing molecular dynamics trajectories using VMD
☆39Updated 10 years ago
Alternatives and similar repositories for md-analysis-tools
Users that are interested in md-analysis-tools are comparing it to the libraries listed below
Sorting:
- Q6 Repository -- EVB, FEP and LIE simulator.☆35Updated 2 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆39Updated 2 years ago
- Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface☆42Updated 4 years ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Updated 10 years ago
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆30Updated last year
- Calculation of water/solvent partition coefficients with Gromacs.☆28Updated last year
- ☆41Updated last year
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆16Updated 3 years ago
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆24Updated last year
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆24Updated 6 years ago
- ☆65Updated 5 months ago
- Analysis of non-covalent interactions in MD trajectories☆65Updated last year
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆49Updated 4 years ago
- Generate coarse-grained molecular dynamics models from atomistic trajectories.☆64Updated last month
- Temperature generator for Replica Exchange MD simulations☆29Updated 3 years ago
- Conformer-Rotamer Ensemble Sampling Tool based on the xtb Semiempirical Extended Tight-Binding Program Package☆34Updated last month
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 3 years ago
- The pDynamo molecular modeling and simulation program☆43Updated last month
- Martini 3 small molecule database☆68Updated 3 months ago
- OpenMM plugin to interface with PLUMED☆73Updated 2 months ago
- A collections of scripts for working molecular dynamics simulations☆45Updated 5 months ago
- Set up relative free energy calculations using a common scaffold☆24Updated 4 months ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆65Updated last year
- Advanced toolkit for binding free energy calculations☆33Updated 4 months ago
- Gromacs Implementation of OPLS-AAM Force field☆14Updated 7 years ago
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆34Updated 6 months ago
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Updated 3 years ago
- Best practice document for alchemical free energy calculations going to livecoms journal☆81Updated last week
- Lee-Ping's general purpose script for running OpenMM molecular dynamics simulations☆32Updated last year
- ☆22Updated 6 months ago