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 last year
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆24Updated 5 months ago
- Useful Collective Variables for OpenMM☆13Updated 11 months ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 3 years ago
- Calculation of water/solvent partition coefficients with Gromacs.☆26Updated 6 months ago
- A collections of scripts for working molecular dynamics simulations☆43Updated 11 months ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆12Updated 6 years 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
- Access to data for workshops and extended tests of MDAnalysis.☆17Updated 7 months ago
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆22Updated 10 months ago
- ☆35Updated 8 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
- Implementation of MOFF force field. Please cite us at Latham, A; Zhang, B J. Chem. Theory Comput. 2021, 17, 3134. (https://pubs.acs.org/d…☆9Updated 2 years ago
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆29Updated last year
- Absolute solvation free energy calculations with OpenFF and OpenMM☆22Updated 5 months ago
- Examples of applications of pymbar to various problems in simulation and experiment☆21Updated 10 years ago
- Tutorials and additional documentation for the WESTPA suite☆14Updated 9 months ago
- Scripts, inputs and the results generated as part of the training the Sage line of OpenFF force fields.☆21Updated last year
- MMTSB Tool Set☆31Updated 6 months ago
- Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits☆12Updated last week
- Example files for Colvars module: https://github.com/Colvars/colvars☆12Updated 3 years ago
- Software tools for fragment-based drug discovery (FBDD)☆27Updated 5 years ago
- Comparison benchmarks between public force fields and Open Force Field Initiative force fields☆10Updated 2 years ago
- In-house tools for setting up arbitrary solute-solvent mixtures for simulation in GROMACS, Amber, OpenMM or other codes☆32Updated 4 years ago
- A simple implementation of replica exchange MD simulations for OpenMM.☆23Updated 3 years ago
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆24Updated 5 years ago
- ☆14Updated 11 months ago
- Compare optimized geometries and energies from various force fields with respect to a QM reference.☆13Updated 4 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆32Updated last year