tbereau / auto_martiniLinks
Automatic MARTINI parametrization of small organic molecules
☆71Updated 7 months ago
Alternatives and similar repositories for auto_martini
Users that are interested in auto_martini are comparing it to the libraries listed below
Sorting:
- Martini 3 small molecule database☆68Updated 3 months ago
- OpenMM plugin to interface with PLUMED☆73Updated 2 months ago
- ☆78Updated last year
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆74Updated 2 years ago
- Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-…☆46Updated last year
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆49Updated 4 years ago
- Generate coarse-grained molecular dynamics models from atomistic trajectories.☆64Updated last month
- Density based object completion over PBC.☆30Updated last year
- A python implementation of the string method with swarms of trajectories using GROMACS☆18Updated 3 years ago
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆46Updated 4 years ago
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆71Updated last week
- A fast solver for large scale MBAR/UWHAM equations☆40Updated last year
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆34Updated 6 months ago
- Experimental and calculated small molecule hydration free energies☆130Updated 3 years ago
- An open source Python framework for transition interface and path sampling calculations.☆116Updated last month
- RESP with inter- and intra-molecular constraints in Psi4.☆32Updated 2 years ago
- Tool for generating MARTINI Polymer itps and structures☆17Updated 5 years ago
- ☆61Updated last month
- 📐 Symmetry-corrected RMSD in Python☆109Updated 3 weeks ago
- Quantum Mechanical Bespoke Force Field Derivation Toolkit☆103Updated last year
- Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface☆42Updated 4 years ago
- MDAnalysis wrapper around Packmol☆36Updated 2 years ago
- ☆25Updated 3 years ago
- Robust Equilibration Detection☆26Updated 4 months ago
- Advanced toolkit for binding free energy calculations☆33Updated 4 months ago
- ☆65Updated 5 months ago
- Best practice document for alchemical free energy calculations going to livecoms journal☆81Updated last week
- An efficient, multithreaded weighted histogram analysis (WHAM) implementation for the post-processing of umbrella MD simulations.☆28Updated last year
- A package for all physics based/related models☆54Updated last year
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆31Updated 2 years ago