arose / simpletrajLinks
Simple library for reading trajectory coordinates
☆18Updated 8 years ago
Alternatives and similar repositories for simpletraj
Users that are interested in simpletraj are comparing it to the libraries listed below
Sorting:
- Sire Molecular Simulations Framework☆96Updated 2 years ago
- Source code for HOLE program.☆35Updated last year
- Weighted Ensemble simulation framework in Python☆56Updated last week
- OpenMM plugin to interface with PLUMED☆67Updated 6 months ago
- Chemical perception tree automated exploration tool.☆19Updated 7 years ago
- HDXer is a package to compute Hydrogen-Deuterium exchange data from biomolecular simulations, compare to experiment, and perform ensemble…☆19Updated 2 years ago
- Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling☆33Updated 2 months ago
- A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations …☆115Updated 6 years ago
- LOOS: a lightweight object-oriented structure analysis library☆125Updated 4 months ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆60Updated last year
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆137Updated last week
- Quickly generate, start and analyze benchmarks for molecular dynamics simulations.☆80Updated 11 months ago
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆44Updated 3 years ago
- An open set of tools for automating tasks relating to small molecules☆68Updated 3 years ago
- pKa estimates for proteins using an ensemble approach☆29Updated last month
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆64Updated 4 years ago
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆70Updated 3 weeks ago
- GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).☆179Updated last month
- (outdated) fork of https://gitlab.com/gromacs/gromacs☆53Updated 2 years ago
- MD trajectory server☆34Updated 2 years ago
- Tools for creating, analyzing and visualizing Conformation Space Networks☆16Updated 3 years ago
- Describe and apply transformation on molecular structures and topologies☆118Updated last week
- A tool for setting up free energy simulations.☆35Updated 2 years ago
- a logistics and persistence engine for the analysis of molecular dynamics trajectories☆30Updated 5 years ago
- Physical validation of molecular simulations☆56Updated last month
- An application for configuring and running simulations with OpenMM☆72Updated last month
- For discussing and aggregating data for force field development☆15Updated 8 years ago
- Dihedral scanner with wavefront propagation☆34Updated 4 months ago
- Best practice document for alchemical free energy calculations going to livecoms journal☆75Updated 2 weeks ago
- Modeling molecular ensembles with scalable data structures and parallel computing☆36Updated last month