SimonBoothroyd / plotmolLinks
Interactive plotting of data annotated with molecule structures.
☆12Updated last year
Alternatives and similar repositories for plotmol
Users that are interested in plotmol are comparing it to the libraries listed below
Sorting:
- Absolute solvation free energy calculations with OpenFF and OpenMM☆22Updated 8 months ago
- Package for consistent reporting of relative free energy results☆39Updated last month
- Algorithms for various Network Layouts and Tooling for planning FE Calculations☆19Updated last week
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 3 years ago
- Scripts, inputs and the results generated as part of the training the Sage line of OpenFF force fields.☆21Updated last month
- Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits☆14Updated 2 weeks ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆27Updated 8 months ago
- An automated framework for generating optimized partial charges for molecules☆38Updated last week
- Compare optimized geometries and energies from various force fields with respect to a QM reference.☆13Updated 4 years ago
- Comparison benchmarks between public force fields and Open Force Field Initiative force fields☆10Updated 2 years ago
- The peleffy (PELE Force Field Yielder) is a Python package that builds PELE-compatible force field templates.☆12Updated 4 months ago
- Repository for Chemical Perception Sampling Tools☆21Updated 11 months ago
- Advanced toolkit for binding free energy calculations☆33Updated last month
- Standalone charge assignment from Espaloma framework.☆40Updated last year
- Differentiably evaluate energies using SMIRNOFF force fields☆17Updated 7 months ago
- Real time monitoring and visualization of Amber MD simulations☆15Updated 5 years ago
- Given an RDKit molecule that does not sanitise, correct it until it does☆41Updated last year
- ☆24Updated last month
- Generate canonical molecule identifiers for quantum chemistry database☆23Updated 4 years ago
- fast functionalisation of molecules☆37Updated 3 years ago
- ☆29Updated 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
- Data and scripts for comprehensive benchmark of conformer relative energies☆25Updated 5 years ago
- ☆32Updated last year
- a high-throughput alchemical free energy execution system for use with HPC, cloud, bare metal, and Folding@Home☆28Updated last 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
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆29Updated last year
- Calculation of water/solvent partition coefficients with Gromacs.☆28Updated 9 months ago
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Updated 2 years ago
- This package contains tools for setting up hybrid-topology FE calculations☆29Updated last month