kassonlab / gmxapi
(outdated) fork of https://gitlab.com/gromacs/gromacs
☆53Updated last year
Alternatives and similar repositories for gmxapi:
Users that are interested in gmxapi are comparing it to the libraries listed below
- ☆52Updated last year
- Analysis of non-covalent interactions in MD trajectories☆53Updated 2 months ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated last year
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆60Updated 3 years ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆58Updated last year
- Set up relative free energy calculations using a common scaffold☆22Updated 6 months ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆31Updated last year
- Accurate prediction of protein pKa with representation learning☆42Updated 3 weeks ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆44Updated 4 years ago
- Wrapper script for preparing explicitly solvated systems for molecular dynamics simulations with Amber.☆16Updated 8 months ago
- INSert membrANE - A simple, versatile tool for building coarse-grained simulation systems☆54Updated 11 months ago
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆43Updated 3 years ago
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆65Updated this week
- An application for configuring and running simulations with OpenMM☆62Updated 4 months ago
- Best practice document for alchemical free energy calculations going to livecoms journal☆68Updated 3 weeks ago
- A general small molecule force field descended from AMBER99 and parm@Frosst, available in the SMIRNOFF format☆28Updated 6 months ago
- ☆33Updated 6 months ago
- Trusted force field files for gromacs☆45Updated 4 months ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆77Updated 9 months ago
- Random Acceleration Molecular Dynamics in GROMACS☆34Updated 7 months ago
- Martini 3 small-molecule database☆57Updated 6 months ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆66Updated last year
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆30Updated last year
- 📐 Symmetry-corrected RMSD in Python☆92Updated 3 months ago
- A fast solver for large scale MBAR/UWHAM equations☆38Updated 6 months ago
- Generate coarse-grained molecular dynamics models from atomistic trajectories.☆61Updated 2 years ago
- Force fields in various formats☆26Updated 10 months ago
- A python toolkit for analysing membrane protein-lipid interactions.☆63Updated last year
- mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data☆32Updated this week
- MDANCE is a flexible n-ary clustering package for all applications.☆51Updated this week