MobleyLab / SeparatedTopologiesLinks
Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).
☆28Updated 8 months ago
Alternatives and similar repositories for SeparatedTopologies
Users that are interested in SeparatedTopologies are comparing it to the libraries listed below
Sorting:
- ☆29Updated 2 weeks ago
- Standalone charge assignment from Espaloma framework.☆40Updated last year
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆32Updated 2 months ago
- ☆44Updated 3 years ago
- Set up relative free energy calculations using a common scaffold☆24Updated this week
- Package for consistent reporting of relative free energy results☆39Updated 2 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
- Absolute solvation free energy calculations with OpenFF and OpenMM☆22Updated 8 months ago
- Machine Learning model for molecular micro-pKa prediction☆43Updated 10 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
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- Python code for generating Boresch restraints from MD simulations☆22Updated 3 years ago
- Scripts, inputs and the results generated as part of the training the Sage line of OpenFF force fields.☆21Updated last month
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- A tutorials suite for BioSimSpace.☆25Updated 3 months ago
- Algorithms for various Network Layouts and Tooling for planning FE Calculations☆19Updated last week
- ☆38Updated 11 months ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆50Updated 4 months ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Updated 10 years ago
- ☆25Updated last year
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated this week
- ☆28Updated 3 months ago
- Advanced toolkit for binding free energy calculations☆33Updated 2 months ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated 2 years ago
- Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits☆14Updated this week
- Software tools for fragment-based drug discovery (FBDD)☆27Updated 5 years ago
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆15Updated 2 years ago
- Calculation of water/solvent partition coefficients with Gromacs.☆28Updated 10 months ago
- ☆15Updated 8 years ago
- Bayesian Multistate Bennett Acceptance Ratio Method☆14Updated last month