tiwarylab / SGOOP
Spectral Gap Optimization of Parameters
☆17Updated 4 years ago
Alternatives and similar repositories for SGOOP:
Users that are interested in SGOOP are comparing it to the libraries listed below
- Enhanced sampling methods for molecular dynamics simulations☆36Updated 2 years ago
- A fast solver for large scale MBAR/UWHAM equations☆38Updated 6 months ago
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆24Updated 4 years ago
- Automatic Mutual Information Noise Omission☆14Updated 5 months ago
- A simple implementation of replica exchange MD simulations for OpenMM.☆23Updated 3 years ago
- Materials for the 2021 PRACE Workshop @ SurfSARA☆31Updated 3 years ago
- ☆10Updated 5 years ago
- Reweighted Autoencoded Variational Bayes for Enhanced Sampling (RAVE)☆42Updated 4 years ago
- A python implementation of the string method with swarms of trajectories using GROMACS☆18Updated 2 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
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆66Updated last year
- Rigid Body Dynamics with OpenMM☆11Updated 6 years ago
- Temperature generator for Replica Exchange MD simulations☆27Updated 2 years ago
- An example of how to write a plugin for OpenMM☆31Updated last year
- Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits☆12Updated last week
- A python class for building a ZMatrix from a RDKit molecule. We can also do coordinate transformations between ZMatrix and Cartesian spac…☆14Updated 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…☆52Updated 10 months ago
- Physical validation of molecular simulations☆56Updated 2 months ago
- Bayesian tools for fitting molecular mechanics torsion parameters to quantum chemical data.☆20Updated 3 years ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆44Updated 4 years ago
- Python code for generating Boresch restraints from MD simulations☆19Updated 2 years ago
- Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations☆20Updated 7 years ago
- A python package for performing GROMACS simulation ensembles☆13Updated this week
- Dihedral scanner with wavefront propagation☆33Updated 11 months ago
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆66Updated this week
- Supporting data for the manuscript "Deep learning the slow modes for rare events sampling"☆19Updated 9 months ago
- Examples of applications of pymbar to various problems in simulation and experiment☆20Updated 10 years ago
- Fast PBC wrapping and unwrapping for VMD☆23Updated 3 months ago
- OpenMM plugin to define forces with neural networks☆32Updated 5 years ago
- Collective variables by artificial neural networks☆9Updated 3 years ago