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
- 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.☆64Updated this week
- Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling☆33Updated 2 years ago
- A physical property evaluation toolkit from the Open Forcefield Consortium.☆56Updated this week
- Physical validation of molecular simulations☆56Updated last month
- Advanced toolkit for binding free energy calculations☆32Updated 2 months ago
- Source code for HOLE program.☆33Updated 6 months ago
- OpenMM plugin to interface with PLUMED☆66Updated this week
- A tool for setting up free energy simulations.☆35Updated 2 years ago
- Analysis of non-covalent interactions in MD trajectories☆53Updated 2 months ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆65Updated last year
- Tools for creating, analyzing and visualizing Conformation Space Networks☆16Updated 2 years ago
- Chemical perception tree automated exploration tool.☆19Updated 6 years ago
- Generate coarse-grained molecular dynamics models from atomistic trajectories.☆61Updated 2 years ago
- (outdated) fork of https://gitlab.com/gromacs/gromacs☆53Updated last year
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆58Updated last year
- Dihedral scanner with wavefront propagation☆32Updated 11 months ago
- Automatic MARTINI parametrization of small organic molecules☆65Updated 3 months ago
- Weighted Ensemble simulation framework in Python☆54Updated last month
- Sire Molecular Simulations Framework☆94Updated last year
- A general small molecule force field descended from AMBER99 and parm@Frosst, available in the SMIRNOFF format☆28Updated 5 months ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆59Updated 3 years ago
- ☆21Updated 4 years ago
- Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations☆20Updated 6 years ago
- Package for consistent reporting of relative free energy results☆37Updated last month
- MD trajectory server☆34Updated last year
- mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data☆32Updated this week
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated last year
- Q6 Repository -- EVB, FEP and LIE simulator.☆31Updated last year
- Best practice document for alchemical free energy calculations going to livecoms journal☆67Updated 2 weeks ago