Becksteinlab / hopLinks
Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.
☆14Updated 7 years ago
Alternatives and similar repositories for hop
Users that are interested in hop are comparing it to the libraries listed below
Sorting:
- Lee-Ping's general purpose script for running OpenMM molecular dynamics simulations☆29Updated last year
- Calculation of water/solvent partition coefficients with Gromacs.☆28Updated 11 months ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 3 years ago
- Constant pH simulation with OpenMM☆13Updated 5 months ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated 2 years ago
- Advanced toolkit for binding free energy calculations☆33Updated 2 weeks ago
- Useful Collective Variables for OpenMM☆14Updated last year
- Absolute solvation free energy calculations with OpenFF and OpenMM☆24Updated 9 months ago
- In-house tools for setting up arbitrary solute-solvent mixtures for simulation in GROMACS, Amber, OpenMM or other codes☆33Updated 4 years ago
- Tutorials and additional documentation for the WESTPA suite☆14Updated last year
- Package for consistent reporting of relative free energy results☆39Updated 2 weeks ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Updated 10 years ago
- Tools for creating, analyzing and visualizing Conformation Space Networks☆16Updated 3 years ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆28Updated 9 months ago
- Set up relative free energy calculations using a common scaffold☆24Updated last month
- Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits☆14Updated this week
- Example files for Colvars module: https://github.com/Colvars/colvars☆13Updated 3 years ago
- Comparison benchmarks between public force fields and Open Force Field Initiative force fields☆10Updated 2 years ago
- ☆11Updated 3 years ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆34Updated last year
- Real time monitoring and visualization of Amber MD simulations☆15Updated 5 years ago
- User Guide for MDAnalysis☆27Updated this week
- Gromacs Implementation of OPLS-AAM Force field☆14Updated 7 years ago
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆23Updated last year
- Interactive plotting of data annotated with molecule structures.☆12Updated last year
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Updated 6 years ago
- Temperature generator for Replica Exchange MD simulations☆29Updated 2 years ago
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3