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:
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆40Updated last month
- Analysis of non-covalent interactions in MD trajectories☆63Updated 9 months ago
- ☆39Updated last year
- Random Acceleration Molecular Dynamics in GROMACS☆39Updated last year
- ☆65Updated 2 months ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated 2 years ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆22Updated 5 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆18Updated 2 years ago
- Temperature generator for Replica Exchange MD simulations☆29Updated 2 years 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
- ☆34Updated 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
- Free Parametrization for Small Molecules☆36Updated last week
- A collections of scripts for working molecular dynamics simulations☆44Updated 2 months ago
- ☆56Updated 2 years ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆84Updated 2 months ago
- MDANCE is a flexible n-ary clustering package for all applications.☆79Updated last week
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆72Updated 2 years ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆53Updated 6 months ago
- ☆30Updated 2 months ago
- Tools to build coarse grained models and perform simulations with OpenMM☆24Updated 2 years ago
- Robust Equilibration Detection☆25Updated last month
- A tutorials suite for BioSimSpace.☆27Updated 5 months ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆60Updated last year
- Standalone charge assignment from Espaloma framework.☆40Updated last year
- An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics☆15Updated 3 years ago
- Different run and analysis scripts as described in the research guides.☆13Updated 3 years ago