GoMartini3-tools / Native-contacts-determination-from-MDLinks
We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU approach (http://pomalab.ippt.pan.pl/GoContactMap/).
☆16Updated last year
Alternatives and similar repositories for Native-contacts-determination-from-MD
Users that are interested in Native-contacts-determination-from-MD 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 6 years ago
- ☆39Updated last year
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆42Updated 2 weeks ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆31Updated 2 years ago
- Random Acceleration Molecular Dynamics in GROMACS☆40Updated last year
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆39Updated 2 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- Analysis of non-covalent interactions in MD trajectories☆65Updated 11 months ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆49Updated 4 years ago
- A tutorials suite for BioSimSpace.☆31Updated last month
- Force Fields☆66Updated 10 months ago
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆16Updated 3 years ago
- ☆58Updated 2 years ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆72Updated 2 months ago
- A collections of scripts for working molecular dynamics simulations☆44Updated 4 months ago
- ☆30Updated 2 weeks ago
- Free Parametrization for Small Molecules☆49Updated 2 months ago
- ☆25Updated last year
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆18Updated 2 years ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆89Updated 4 months ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆18Updated 2 months ago
- An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics☆17Updated 3 years ago
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆32Updated 6 months ago
- ☆65Updated 4 months ago
- Useful Collective Variables for OpenMM☆17Updated last year
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago
- Standalone charge assignment from Espaloma framework.☆45Updated 2 months ago
- A simple implementation of replica exchange MD simulations for OpenMM.☆24Updated 4 years ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Updated 10 years ago
- ☆34Updated last year