[gmx-users] Pushing the pulled ligand into the binding pocket

Ayesha Fatima ayeshafatima.69 at gmail.com
Wed May 6 09:59:06 CEST 2015

Dear Gromacs users,
I have just started using gromacs 5.0.4 for steered dynamics and am running
a setup for pulling my ligand out of the binding pocket. It is still
running but a few questions to the users since this method is being used
very frequently.

1) I have pulled my ligand in the +z direction but used the
pull_geometry=distance. Now to push it back into the pocket what should be
the code? Is it the same or i have to to use pull_geometry=direction and
give a direction vector? I checked the mailing list but could not find a
satisfactory answer.

2) has anyone used the g_mmpbsa program? I would like to learn from
someone's experience.

Thank you
Ayesha Fatima
PhD (UM)

More information about the gromacs.org_gmx-users mailing list