search

HITS-MCM / gromacs-ramd

Random Acceleration Molecular Dynamics in GROMACS
GNU Lesser General Public License v2.1
32 stars 7 forks source link

Acclerating only a part of the ligand #28

Open kellegra opened 2 years ago

kellegra commented 2 years ago

Hi there,

is it actually possible to only accelerate a part of the ligand? I have a relatively long ligand buried in a kind of tunnel in the protein. It looks like, that a polar interaction on one end of the ligand leads to overestimating the residence time. The ligand is sometimes "rotating" in the tunnel and forces the binding pocket to open in a unlikely way. Now I would like to only accelerate the end with the polar interactions, to see, what influence this would have on the residence time and the exit path as well.

Best regards, Gerald

BerndDoser commented 2 years ago

From a technical point of view this should be possible be defining a new group in the idx-file and use it instead of the whole ligand group.