DEShawResearch / msys
Tools for preparation and analysis of systems for molecular dynamics.
☆24Updated 2 years ago
Alternatives and similar repositories for msys:
Users that are interested in msys are comparing it to the libraries listed below
- ☆43Updated 3 years ago
- Package for consistent reporting of relative free energy results☆37Updated 2 months ago
- Given an RDKit molecule that does not sanitise, correct it until it does☆37Updated 11 months ago
- 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…☆52Updated 10 months ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆23Updated 3 months ago
- Differentiably evaluate energies using SMIRNOFF force fields☆16Updated 3 months ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 2 years ago
- Endstate corrections from MM to QML potential☆12Updated last year
- Enhanced sampling methods for molecular dynamics simulations☆36Updated 2 years ago
- Rigid Body Dynamics with OpenMM☆11Updated 6 years ago
- A simple implementation of replica exchange MD simulations for OpenMM.☆23Updated 3 years ago
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆29Updated 5 years ago
- Scripts, inputs and the results generated as part of the training the Sage line of OpenFF force fields.☆21Updated last year
- Equivariant GNN for the prediction of atomic multipoles up to quadrupoles.☆29Updated 2 years ago
- Standalone charge assignment from Espaloma framework.☆39Updated 8 months ago
- Dihedral scanner with wavefront propagation☆33Updated 11 months ago
- OpenFF NAGL☆16Updated this week
- a high-throughput alchemical free energy execution system for use with HPC, cloud, bare metal, and Folding@Home☆26Updated this week
- A machine learned Molecular Mechanics force field with integration into GROMACS and OpenMM☆38Updated this week
- Transferable Double Exponential non-bonded potential for condensed phase simulations of small molecules☆22Updated 7 months ago
- Best practice document for alchemical free energy calculations going to livecoms journal☆68Updated 3 weeks ago
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆43Updated 3 years ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- Examples of applications of pymbar to various problems in simulation and experiment☆20Updated 10 years ago
- Source code and input files associated to the paper "Targeted free energy perturbation revisited: Accurate free energies from mapped refe…☆13Updated 3 years ago
- RESP with inter- and intra-molecular constraints in Psi4.☆30Updated last year
- A physical property evaluation toolkit from the Open Forcefield Consortium.☆56Updated this week
- ☆21Updated 4 years ago
- Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits☆12Updated 3 weeks ago
- Example to fit parameters and run CG simulations using TorchMD and Schnet☆43Updated 3 years ago