weitse-hsu / enhanced_sampling_tutorialsLinks
A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling methods using GROMACS
☆20Updated 11 months ago
Alternatives and similar repositories for enhanced_sampling_tutorials
Users that are interested in enhanced_sampling_tutorials 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
- Enhanced sampling methods for molecular dynamics simulations☆38Updated 2 years ago
- Repository for MD methods and analysis from submitted or published work☆19Updated 2 years ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Updated 10 years ago
- Useful Collective Variables for OpenMM☆14Updated last year
- Temperature generator for Replica Exchange MD simulations☆29Updated 2 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
- A simple implementation of replica exchange MD simulations for OpenMM.☆23Updated 4 years ago
- Workshop - Analysis of Molecular Dynamics Simulation Using Python☆19Updated 5 years ago
- Build coarse-grained mapping for molecules from a web-GUI☆14Updated 3 years ago
- ☆12Updated last year
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆40Updated this week
- ☆38Updated 11 months ago
- scripts for analyzing molecular dynamics trajectories using VMD☆39Updated 10 years ago
- Calculation of water/solvent partition coefficients with Gromacs.☆28Updated 10 months ago
- Convenience functions for VMD-TCL scripting☆14Updated last month
- 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
- easyPARM is a computational tool developed to simplify the derivation of force field parameters for metal-containing molecular systems an…☆25Updated last month
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated 2 years ago
- Python package to construct free energy profiles from biased molecular simulation data using both log-likelihood maximization and self-co…☆20Updated last year
- Set of tools to generate a multi-eGO force field to perform molecular dynamics simulations☆14Updated last month
- ☆40Updated 2 years ago
- Absolute solvation free energy calculations with OpenFF and OpenMM☆23Updated 8 months ago
- ☆10Updated 5 years ago
- Multiscale Simulation Tool for Backmapping☆18Updated 2 weeks ago
- Tools to build coarse grained models and perform simulations with OpenMM☆24Updated 2 years ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Updated 6 years ago
- A collections of scripts for working molecular dynamics simulations☆44Updated 3 weeks ago
- A tutorials suite for BioSimSpace.☆25Updated 3 months ago
- Example files for Colvars module: https://github.com/Colvars/colvars☆13Updated 3 years ago