MobleyLab / SeparatedTopologies
Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).
☆24Updated 5 months ago
Alternatives and similar repositories for SeparatedTopologies:
Users that are interested in SeparatedTopologies are comparing it to the libraries listed below
- ☆27Updated last month
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- Standalone charge assignment from Espaloma framework.☆39Updated 9 months ago
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆31Updated last month
- ☆43Updated 3 years ago
- Package for consistent reporting of relative free energy results☆39Updated last week
- Set up relative free energy calculations using a common scaffold☆22Updated 2 weeks ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆29Updated 2 months ago
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆18Updated 2 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- A collection of notebooks and scripts for the prediction of follow-up compounds in☆11Updated 4 months ago
- ☆26Updated last year
- This package contains tools for setting up hybrid-topology FE calculations☆28Updated last week
- ☆35Updated 8 months ago
- ☆15Updated 8 years ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- OpenFF NAGL☆16Updated 2 weeks ago
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆32Updated 5 years ago
- Software tools for fragment-based drug discovery (FBDD)☆27Updated 5 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated 3 weeks ago
- Scripts, inputs and the results generated as part of the training the Sage line of OpenFF force fields.☆21Updated last year
- Given an RDKit molecule that does not sanitise, correct it until it does☆41Updated last year
- Absolute solvation free energy calculations with OpenFF and OpenMM☆22Updated 5 months ago
- A tutorials suite for BioSimSpace.☆25Updated 3 weeks ago
- Advanced toolkit for binding free energy calculations☆32Updated 4 months ago
- Python code for generating Boresch restraints from MD simulations☆20Updated 2 years ago
- 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…☆53Updated last year
- a high-throughput alchemical free energy execution system for use with HPC, cloud, bare metal, and Folding@Home☆27Updated this week
- ☆45Updated 4 years ago
- ☆25Updated last year