GMPavanLab / Swarm-CG
Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization
☆45Updated 8 months ago
Alternatives and similar repositories for Swarm-CG:
Users that are interested in Swarm-CG are comparing it to the libraries listed below
- Tool for generating MARTINI Polymer itps and structures☆15Updated 4 years ago
- OpenMM plugin to interface with PLUMED☆66Updated 2 months ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆67Updated last year
- Ensembler is a python package that provides fast and easy access to 1D and 2D model system simulations. It can be used for method develop…☆53Updated last year
- Automatic MARTINI parametrization of small organic molecules☆66Updated 5 months ago
- ☆64Updated last year
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆67Updated this week
- Martini 3 small-molecule database☆59Updated 8 months ago
- ☆35Updated 8 months ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆45Updated 4 years ago
- Physical validation of molecular simulations☆56Updated 3 weeks ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- A physical property evaluation toolkit from the Open Forcefield Consortium.☆56Updated this week
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆32Updated last year
- Poltype 2: Automated Parameterization for AMOEBA☆45Updated this week
- ☆54Updated 2 years ago
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆24Updated 5 years ago
- A python implementation of the string method with swarms of trajectories using GROMACS☆18Updated 2 years ago
- A simple implementation of replica exchange MD simulations for OpenMM.☆23Updated 3 years ago
- Generate coarse-grained molecular dynamics models from atomistic trajectories.☆63Updated 2 years ago
- ☆25Updated 3 years ago
- Package for consistent reporting of relative free energy results☆39Updated last week
- ☆10Updated 5 years ago
- Enhanced sampling methods for molecular dynamics simulations☆36Updated 2 years ago
- A comprehensive toolkit for predicting free energies☆52Updated 3 months ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆58Updated last year
- Advanced toolkit for binding free energy calculations☆32Updated 4 months ago
- ASH is a Python-based computational chemistry and QM/MM environment, primarily for molecular calculations in the gas phase, explicit sol…☆70Updated this week
- Reweighted Autoencoded Variational Bayes for Enhanced Sampling (RAVE)☆43Updated 5 years ago
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆43Updated 3 years ago