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:
- OpenMM plugin to interface with PLUMED☆69Updated 8 months ago
- LOOS: a lightweight object-oriented structure analysis library☆125Updated last week
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆142Updated last week
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆44Updated 4 years ago
- INSert membrANE - A simple, versatile tool for building coarse-grained simulation systems☆67Updated last year
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆66Updated 4 years ago
- Create coarse grain Martini input files for Gromacs from (atomistic) pdb files.☆38Updated 2 years ago
- Best practice document for alchemical free energy calculations going to livecoms journal☆78Updated 3 weeks ago
- A stripped-down set of just antechamber, sqm, and tleap.☆33Updated 4 years ago
- A fast solver for large scale MBAR/UWHAM equations☆40Updated last year
- Quickly generate, start and analyze benchmarks for molecular dynamics simulations.☆80Updated last year
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆61Updated last year
- A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations …☆115Updated 6 years ago
- An open source Python framework for transition interface and path sampling calculations.☆115Updated 4 months ago
- An open set of tools for automating tasks relating to small molecules☆68Updated 4 years ago
- Generate coarse-grained molecular dynamics models from atomistic trajectories.☆64Updated 2 years ago
- Weighted Ensemble simulation framework in Python☆58Updated 2 weeks ago
- An application for configuring and running simulations with OpenMM☆74Updated 2 weeks ago
- (outdated) fork of https://gitlab.com/gromacs/gromacs☆53Updated 2 years ago
- A tool for setting up free energy simulations.☆36Updated 3 years ago
- Describe and apply transformation on molecular structures and topologies☆126Updated last week
- GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).☆181Updated last month
- A physical property evaluation toolkit from the Open Forcefield Consortium.☆56Updated 2 weeks ago
- A general small molecule force field descended from AMBER99 and parm@Frosst, available in the SMIRNOFF format☆30Updated last year
- Source code for HOLE program.☆36Updated last year
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆34Updated 4 months ago
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆70Updated 3 weeks ago
- Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling☆34Updated 2 weeks ago
- Systematic force field optimization.☆154Updated 10 months ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆160Updated 2 months ago