Becksteinlab / MDPOW
Calculation of water/solvent partition coefficients with Gromacs.
☆26Updated 4 months ago
Alternatives and similar repositories for MDPOW:
Users that are interested in MDPOW are comparing it to the libraries listed below
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆22Updated 2 months ago
- Python code for generating Boresch restraints from MD simulations☆18Updated 2 years ago
- Scripts, inputs and the results generated as part of the training the Sage line of OpenFF force fields.☆20Updated last year
- Package for consistent reporting of relative free energy results☆37Updated last month
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 2 years ago
- Advanced toolkit for binding free energy calculations☆32Updated last month
- ☆43Updated 3 years ago
- ☆32Updated 5 months ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆58Updated last year
- Standalone charge assignment from Espaloma framework.☆38Updated 7 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
- The peleffy (PELE Force Field Yielder) is a Python package that builds PELE-compatible force field templates.☆12Updated 2 months ago
- The MDAnalysis Toolkits Registry☆17Updated this week
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆36Updated last year
- Analysis of non-covalent interactions in MD trajectories☆51Updated last month
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆29Updated 5 years ago
- In-house tools for setting up arbitrary solute-solvent mixtures for simulation in GROMACS, Amber, OpenMM or other codes☆32Updated 4 years ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆31Updated last year
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆24Updated 4 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- Stable version of MCCE.☆10Updated 4 months ago
- Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits☆11Updated last week
- Temperature generator for Replica Exchange MD simulations☆27Updated 2 years ago
- Given an RDKit molecule that does not sanitise, correct it until it does☆37Updated 10 months ago
- Set up relative free energy calculations using a common scaffold☆22Updated 5 months ago
- ☆13Updated 5 years ago
- A python class for building a ZMatrix from a RDKit molecule. We can also do coordinate transformations between ZMatrix and Cartesian spac…☆13Updated last year
- Ensembler is a python package that provides fast and easy access to 1D and 2D model system simulations. It can be used for method develop…☆52Updated 9 months ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆30Updated last year
- This package contains tools for setting up hybrid-topology FE calculations☆26Updated last month