Targeted molecular dynamics (TMD)

User discussions
1

Dear all,
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.

Thanking you,

Kalyan

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

2

The authors report that they are using the pull code to carry out biased simulations. There is a tutorial for the pull code at http://www.mdtutorials.com/gmx/umbrella/index.html but GROMACS doesn’t support TMD in a general sense as some other software packages do.

If you can’t reproduce what the authors did, ask them for example inputs. Note, however, that they are using obsolete versions of GROMACS so .mdp keywords will have changed.

3

Dear Professor Justin Lemkul,
Thank you very much for your reply and suggestion.

Sincerely yours,
Kalyan