dmzuckerman / Sampling-UncertaintyLinks
Best Practices article intended for LiveCoMS
☆41Updated 5 years ago
Alternatives and similar repositories for Sampling-Uncertainty
Users that are interested in Sampling-Uncertainty are comparing it to the libraries listed below
Sorting:
- Generate coarse-grained molecular dynamics models from atomistic trajectories.☆64Updated 2 years ago
- Physical validation of molecular simulations☆56Updated last month
- An example of how to write a plugin for OpenMM☆31Updated last year
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆42Updated 3 years ago
- Database of hand-built OPLS-AA parameters and topologies for 464 molecules. Zip files contains parameter and topologies for OpenMM, Groma…☆33Updated 6 years ago
- Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations☆20Updated 7 years ago
- Python library for adaptive QM/MM methods☆28Updated 5 years ago
- A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations …☆114Updated 6 years ago
- Suite of programs to perform non-linear dimensionality reduction -- sketch-map in particular☆46Updated 8 months ago
- OpenMM plugin to interface with PLUMED☆66Updated 3 months ago
- Automatic MARTINI parametrization of small organic molecules☆66Updated this week
- Martini 3 small-molecule database☆60Updated 9 months ago
- A fast solver for large scale MBAR/UWHAM equations☆39Updated 8 months ago
- Package for reading, analysis and visualization of metadynamics HILLS☆34Updated last year
- Reads Gromacs EDR file to populate a pandas dataframe☆33Updated 6 months ago
- scripts for analyzing molecular dynamics trajectories using VMD☆38Updated 10 years ago
- A general small molecule force field descended from AMBER99 and parm@Frosst, available in the SMIRNOFF format☆29Updated 8 months ago
- Fast PBC wrapping and unwrapping for VMD☆23Updated 6 months ago
- Materials for the 2021 PRACE Workshop @ SurfSARA☆30Updated 3 years ago
- (outdated) fork of https://gitlab.com/gromacs/gromacs☆53Updated 2 years ago
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆69Updated 2 weeks ago
- OpenMM plugin to define forces with neural networks☆32Updated 5 years ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆45Updated 4 years ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆31Updated last year
- Experimental small molecule hydration free energy dataset☆30Updated 3 years ago
- Enhanced sampling methods for molecular dynamics simulations☆36Updated 2 years ago
- RESP with inter- and intra-molecular constraints in Psi4.☆31Updated 2 years ago
- A comprehensive tool for analyzing liquid solvation structure.☆52Updated 10 months ago
- ☆66Updated 5 months ago
- Analyse Rotational Diffusion Tensor from MD Simulations☆18Updated 7 months ago