MobleyLab / SolvationToolkit
In-house tools for setting up arbitrary solute-solvent mixtures for simulation in GROMACS, Amber, OpenMM or other codes
☆31Updated 4 years ago
Related projects ⓘ
Alternatives and complementary repositories for SolvationToolkit
- ☆41Updated 2 years ago
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆27Updated 4 years ago
- Standalone charge assignment from Espaloma framework.☆38Updated 3 months ago
- Package for consistent reporting of relative free energy results☆37Updated 5 months ago
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆61Updated this week
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆41Updated 3 years ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆22Updated last year
- Given an RDKit molecule that does not sanitise, correct it until it does☆36Updated 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
- Advanced toolkit for binding free energy calculations☆31Updated 3 weeks ago
- ☆31Updated 2 months ago
- RESP with inter- and intra-molecular constraints in Psi4.☆29Updated last year
- Compare optimized geometries and energies from various force fields with respect to a QM reference.☆13Updated 3 years ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆30Updated last year
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆34Updated last year
- ☆26Updated 10 months ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆37Updated last year
- A command line application to launch molecular dynamics simulations with OpenMM☆39Updated 2 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
- ☆25Updated 3 weeks 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…☆51Updated 6 months ago
- Set up relative free energy calculations using a common scaffold☆22Updated 2 months ago
- Dihedral scanner with wavefront propagation☆31Updated 7 months ago
- Toolkit for open antiviral drug discovery by the ASAP Discovery Consortium☆30Updated this week
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆27Updated 9 months ago
- Best practice document for alchemical free energy calculations going to livecoms journal☆63Updated 3 weeks ago
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆23Updated 4 years ago
- Conformer-Rotamer Ensemble Sampling Tool based on the xtb Semiempirical Extended Tight-Binding Program Package☆28Updated 3 weeks ago
- A comprehensive toolkit for predicting free energies☆50Updated 2 weeks ago