Becksteinlab / hop
Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.
☆14Updated 6 years ago
Alternatives and similar repositories for hop:
Users that are interested in hop are comparing it to the libraries listed below
- Lee-Ping's general purpose script for running OpenMM molecular dynamics simulations☆27Updated 11 months ago
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆18Updated 2 years ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 3 years ago
- ☆11Updated 2 years ago
- Convenience functions for VMD-TCL scripting☆14Updated 4 months ago
- scripts for analyzing molecular dynamics trajectories using VMD☆38Updated 9 years ago
- Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits☆12Updated this week
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆24Updated 4 months ago
- Useful Collective Variables for OpenMM☆13Updated 11 months ago
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆24Updated 4 years ago
- Tools for creating, analyzing and visualizing Conformation Space Networks☆16Updated 2 years ago
- Gromacs Implementation of OPLS-AAM Force field☆13Updated 6 years ago
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆29Updated last year
- User Guide for MDAnalysis☆25Updated this week
- Calculation of water/solvent partition coefficients with Gromacs.☆26Updated 6 months ago
- Workshop - Analysis of Molecular Dynamics Simulation Using Python☆17Updated 4 years ago
- Advanced toolkit for binding free energy calculations☆32Updated 3 months ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆12Updated 6 years ago
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆26Updated 2 weeks ago
- In-house tools for setting up arbitrary solute-solvent mixtures for simulation in GROMACS, Amber, OpenMM or other codes☆32Updated 4 years ago
- We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…☆16Updated 9 months ago
- ☆26Updated 3 weeks ago
- Analysis of non-covalent interactions in MD trajectories☆55Updated 3 months ago
- ☆33Updated 7 months ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆22Updated 5 years ago
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆32Updated 5 years ago
- Density based object completion over PBC.☆29Updated 4 months ago
- Absolute solvation free energy calculations with OpenFF and OpenMM☆22Updated 4 months ago
- ☆26Updated last year