I would like to perform targeted molecular dynamics (TMD) simulation to explore a translocation process of a ligand molecule. I have gone through a few articles [J. Chem. Inf. Model. 2019, 59, 5135−5147, and J. Chem. Theory Comput. 2018, 14, 6175−6182], where TMD was carried out using Gromacs. Is there any Gromacs-TMD tutorial available?
I am looking forward to your suggestions.
PS: I didn’t get an expected result with TMD using Plumed-Gromacs for this particular system!
GROMACS version: 5.1.4
GROMACS modification: Yes/No