MikkelDA / COBY
COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3
☆28Updated last month
Alternatives and similar repositories for COBY:
Users that are interested in COBY 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 10 months ago
- ☆35Updated 8 months ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆24Updated 5 years ago
- ☆26Updated last year
- A tutorials suite for BioSimSpace.☆25Updated 3 weeks ago
- Standalone charge assignment from Espaloma framework.☆39Updated 9 months ago
- ☆27Updated last month
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆18Updated 2 years ago
- Weighted Ensemble Data Analysis and Plotting☆24Updated 7 months ago
- A simple implementation of replica exchange MD simulations for OpenMM.☆23Updated 3 years ago
- Temperature generator for Replica Exchange MD simulations☆28Updated 2 years ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 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
- Package for consistent reporting of relative free energy results☆39Updated last week
- 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☆13Updated 6 years ago
- A collections of scripts for working molecular dynamics simulations☆43Updated 11 months ago
- RESP with inter- and intra-molecular constraints in Psi4.☆31Updated last year
- Toolkit for open antiviral drug discovery by the ASAP Discovery Consortium☆37Updated 3 weeks ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated 6 months ago
- Tools to build coarse grained models and perform simulations with OpenMM☆23Updated 2 years ago
- Cryptic pocket prediction using AlphaFold 2☆22Updated 2 years ago
- Density based object completion over PBC.☆29Updated 4 months ago
- ☆15Updated 3 years ago
- Useful Collective Variables for OpenMM☆13Updated 11 months ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆24Updated 5 months ago
- Python code for generating Boresch restraints from MD simulations☆20Updated 2 years ago
- ☆25Updated last year
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆15Updated last year