LucyJimenez / MDanalysis_WorkshopLinks
Workshop - Analysis of Molecular Dynamics Simulation Using Python
☆19Updated 4 years ago
Alternatives and similar repositories for MDanalysis_Workshop
Users that are interested in MDanalysis_Workshop are comparing it to the libraries listed below
Sorting:
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆22Updated 5 years ago
- ☆37Updated 11 months 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 last year
- User Guide for MDAnalysis☆28Updated this week
- scripts for analyzing molecular dynamics trajectories using VMD☆39Updated 10 years ago
- Package for consistent reporting of relative free energy results☆39Updated last month
- Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits☆14Updated 3 weeks ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 3 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
- Useful Collective Variables for OpenMM☆14Updated last year
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆24Updated 5 years ago
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆29Updated last year
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆27Updated 8 months ago
- Analysis of non-covalent interactions in MD trajectories☆59Updated 7 months ago
- Standalone charge assignment from Espaloma framework.☆40Updated last year
- Temperature generator for Replica Exchange MD simulations☆28Updated 2 years ago
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆40Updated 2 weeks ago
- A tutorials suite for BioSimSpace.☆25Updated 3 months ago
- ☆16Updated last week
- ☆15Updated 3 years ago
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Updated 2 years ago
- Gromacs Implementation of OPLS-AAM Force field☆14Updated 7 years ago
- Absolute solvation free energy calculations with OpenFF and OpenMM☆22Updated 8 months ago
- Set up relative free energy calculations using a common scaffold☆24Updated 3 months ago
- A collections of scripts for working molecular dynamics simulations☆44Updated last week
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Updated 6 years ago
- This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and an…☆16Updated last year
- Examples of applications of pymbar to various problems in simulation and experiment☆22Updated 10 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated last year
- Materials for 0.5-day MDAnalysis workshops☆11Updated 2 weeks ago