[gmx-users] what's the easiest way to generate a md trajectory for ligand flying into/being pulled out of the pocket?

[Barnett, James W]

Look into the pull code. You'll want to choose two groups (one for the ligand, one for the binding site), and one coordinate with those groups where the pull rate is not zero (negative rate to bring them together, positive rate to pull them apart).

--
James “Wes” Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow
Chemical and Biomolecular Engineering

Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarnet4 at tulane.edu


________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Victor Ma <victordsmagift at gmail.com>
Sent: Wednesday, August 26, 2015 12:31 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] what's the easiest way to generate a md trajectory for ligand flying into/being pulled out of the pocket?

hello all

I got a urgent request to make a MD movie for pulling the ligand out of the
binding site/or the ligand flying into the pocket . I feel like i need to
run something like steered md, which I've never done before. So can anyone
please suggest a quick and "dirty" way to generate such a movie?

Thank you!!

Victor
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