ghorbanimahdi73 / GraphVampNet
☆15Updated 3 years ago
Alternatives and similar repositories for GraphVampNet:
Users that are interested in GraphVampNet are comparing it to the libraries listed below
- 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 9 months ago
- Temperature generator for Replica Exchange MD simulations☆28Updated 2 years ago
- ☆64Updated last year
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- A simple implementation of replica exchange MD simulations for OpenMM.☆23Updated 3 years ago
- ☆34Updated 7 months ago
- A python implementation of the string method with swarms of trajectories using GROMACS☆18Updated 2 years ago
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆26Updated 3 weeks ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆45Updated 4 years ago
- Enhanced sampling methods for molecular dynamics simulations☆36Updated 2 years ago
- ☆43Updated 3 years ago
- A collections of scripts for working molecular dynamics simulations☆43Updated 11 months ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆15Updated last year
- ☆54Updated last year
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆24Updated 4 years ago
- Repository for MD methods and analysis from submitted or published work☆17Updated last year
- ☆11Updated 10 months ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆28Updated last month
- Supporting data for the manuscript "Deep learning the slow modes for rare events sampling"☆20Updated 10 months ago
- Random Acceleration Molecular Dynamics in GROMACS☆36Updated 9 months ago
- Tools to build coarse grained models and perform simulations with OpenMM☆22Updated 2 years ago
- ☆21Updated 7 months ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated last year
- Different run and analysis scripts as described in the research guides.☆13Updated 2 years ago
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆32Updated 5 years ago
- ☆26Updated last year
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆31Updated last year
- MDAnalysis tool to calculate membrane curvature.☆32Updated 8 months ago
- Entropy from PDB conformational ensembles☆7Updated last year
- Implicit Solvent Approach Based on Generalised Born and Transferable Graph Neural Networks for Molecular Dynamics Simulations☆33Updated last week