dcTMD calculations with GROMACS
Perform dcTMD free energy simulations and calculations
- Author(s):
- Release: 0.1.5
- License: MIT
- UniqueID: 7950b716-2bc9-4cb6-8472-6506c702adea
GROMACS dcTMD free energy calculation
Perform an ensemble of targeted MD simulations of a user-specified size using the GROMACS PULL code and calculate dcTMD free energy and friction profiles for the resulting dissocation pathway. Note that pathway separation is not performed by the workflow; the user is responsible for checking the ensemble themselves.
The input protein (PDB) and ligand (SDF) files provided are parameterized by the 'Protein-ligand complex parameterization' subworkflow.
Note that the workflow uses a MDP file for configuring the TMD simulations; this
is packaged alongside the workflow as tmd.mdp.
Citations
- Steffen Wolf and Gerhard Stock (2018), Targeted Molecular Dynamics Calculations of Free Energy Profiles Using a Nonequilibrium Friction Correction, J. Chem. Theory Comput. doi:10.1021/acs.jctc.8b00835
- Steffen Wolf, Benjamin Lickert, Simon Bray and Gerhard Stock (2020), Multisecond ligand dissociation dynamics from atomistic simulations, Nat. Commun. doi:10.1038/s41467-020-16655-1