michellab / SireLinks
Sire Molecular Simulations Framework
☆96Updated 2 years ago
Alternatives and similar repositories for Sire
Users that are interested in Sire are comparing it to the libraries listed below
Sorting:
- LOOS: a lightweight object-oriented structure analysis library☆126Updated 2 months ago
- OpenMM plugin to interface with PLUMED☆73Updated 2 months ago
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆46Updated 4 years ago
- INSert membrANE - A simple, versatile tool for building coarse-grained simulation systems☆73Updated last year
- A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations …☆117Updated 7 years ago
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆145Updated 3 weeks ago
- Source code for HOLE program.☆37Updated last year
- Quickly generate, start and analyze benchmarks for molecular dynamics simulations.☆80Updated last year
- GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).☆184Updated 4 months ago
- (outdated) fork of https://gitlab.com/gromacs/gromacs☆53Updated 2 years ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆67Updated 4 years ago
- An application for configuring and running simulations with OpenMM☆76Updated 2 months ago
- Describe and apply transformation on molecular structures and topologies☆130Updated last month
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆63Updated last year
- Create coarse grain Martini input files for Gromacs from (atomistic) pdb files.☆39Updated 3 years ago
- An open set of tools for automating tasks relating to small molecules☆68Updated 4 years ago
- A stripped-down set of just antechamber, sqm, and tleap.☆33Updated 4 years ago
- Best practice document for alchemical free energy calculations going to livecoms journal☆81Updated 2 weeks ago
- Generate coarse-grained molecular dynamics models from atomistic trajectories.☆64Updated last month
- Systematic force field optimization.☆156Updated last year
- Biomolecular simulation trajectory/data analysis.☆162Updated last month
- Quantum Mechanical Bespoke Force Field Derivation Toolkit☆103Updated last year
- Bayesian tools for fitting molecular mechanics torsion parameters to quantum chemical data.☆21Updated 4 years ago
- A fast solver for large scale MBAR/UWHAM equations☆40Updated last year
- An open source Python framework for transition interface and path sampling calculations.☆116Updated 3 weeks ago
- Weighted Ensemble simulation framework in Python☆59Updated last month
- An example of how to write a plugin for OpenMM☆31Updated last year
- Physical validation of molecular simulations☆57Updated this week
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆192Updated 2 years ago
- A general small molecule force field descended from AMBER99 and parm@Frosst, available in the SMIRNOFF format☆31Updated 2 weeks ago