MMGBSA simulation and calculation

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 ...

Protein-ligand complex parameterization

Parameterizes an input protein (PDB) and ligand (SDF) file prior to molecular dynamics simulation with GROMACS.

This is a simple workflow intended for use as a subworkflow in more complex MD workflows. It is used as a subworkflow by the GROMACS MMGBSA and dcTMD workflows.