arose / simpletraj
Simple library for reading trajectory coordinates
☆17Updated 8 years ago
Alternatives and similar repositories for simpletraj:
Users that are interested in simpletraj are comparing it to the libraries listed below
- Source code for HOLE program.☆32Updated 5 months ago
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆63Updated last month
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆42Updated 3 years ago
- A comprehensive toolkit for predicting free energies☆50Updated 3 weeks ago
- OpenMM plugin to interface with PLUMED☆60Updated 2 months ago
- A tool for setting up free energy simulations.☆35Updated 2 years ago
- Physical validation of molecular simulations☆56Updated 3 weeks ago
- Tools for creating, analyzing and visualizing Conformation Space Networks☆16Updated 2 years ago
- A physical property evaluation toolkit from the Open Forcefield Consortium.☆56Updated this week
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆59Updated 3 years ago
- HDXer is a package to compute Hydrogen-Deuterium exchange data from biomolecular simulations, compare to experiment, and perform ensemble…☆19Updated last year
- Chemical perception tree automated exploration tool.☆19Updated 6 years ago
- Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling☆33Updated 2 years ago
- Analysis of non-covalent interactions in MD trajectories☆51Updated 3 weeks ago
- A command line application to launch molecular dynamics simulations with OpenMM☆39Updated 2 years ago
- Automatic MARTINI parametrization of small organic molecules☆63Updated 2 months ago
- In-house tools for setting up arbitrary solute-solvent mixtures for simulation in GROMACS, Amber, OpenMM or other codes☆31Updated 4 years ago
- MD trajectory server☆34Updated last year
- pKa estimates for proteins using an ensemble approach☆27Updated 3 months ago
- Dihedral scanner with wavefront propagation☆32Updated 9 months ago
- Advanced toolkit for binding free energy calculations☆32Updated 3 weeks ago
- Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-…☆44Updated 5 months ago
- ☆51Updated last year
- Weighted Ensemble simulation framework in Python☆52Updated last week
- Generate coarse-grained molecular dynamics models from atomistic trajectories.☆60Updated 2 years ago
- (outdated) fork of https://gitlab.com/gromacs/gromacs☆53Updated last year
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆63Updated last year
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆57Updated 11 months ago
- mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data☆30Updated this week
- Sire Molecular Simulations Framework☆94Updated last year