bussilab / MDRefineLinks
☆16Updated last week
Alternatives and similar repositories for MDRefine
Users that are interested in MDRefine are comparing it to the libraries listed below
Sorting:
- Standalone charge assignment from Espaloma framework.☆40Updated last year
- Tools to build coarse grained models and perform simulations with OpenMM☆24Updated 2 years ago
- Scripts, inputs and the results generated as part of the training the Sage line of OpenFF force fields.☆21Updated last month
- A python implementation of pdb2oniom for QM/MM (ONIOM) calculations☆10Updated last year
- ☆29Updated last year
- Multiscale Simulation Tool for Backmapping☆17Updated 2 weeks ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆22Updated 5 years ago
- Weighted Ensemble Data Analysis and Plotting☆24Updated last month
- ☆37Updated 11 months ago
- A tutorials suite for BioSimSpace.☆25Updated 3 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
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆40Updated 2 weeks ago
- Data set of protein-ligand complexes with reliable experimental structures and affinities☆37Updated 5 months ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆27Updated 8 months ago
- Package for consistent reporting of relative free energy results☆39Updated last month
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆14Updated 3 months ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆29Updated 2 weeks ago
- LAST: Latent Space Assisted Adaptive Sampling for Protein Trajectories☆12Updated 2 years ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Updated 6 years ago
- ☆28Updated last year
- Python module for identification of conserved water molecules from molecular dynamics trajectories.☆12Updated last month
- Repository for the 2024 OpenFE industry benchmark efforts☆22Updated last month
- ☆40Updated 2 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated this week
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆15Updated 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
- Catalyst design for the Morita−Baylis−Hillman Reaction using a graph-based genetic algorithm☆10Updated last year
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- Gromacs Implementation of OPLS-AAM Force field☆14Updated 7 years ago
- Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits☆14Updated 2 weeks ago