[gmx-users] PBC problem in bilayer system

Justin Lemkul jalemkul at vt.edu
Tue Sep 16 02:20:44 CEST 2014

On 9/15/14 3:12 PM, shahab shariati wrote:
> Dear Justin
> Thanks for your answer.
> You said " The raw output of g_traj in this case is not very useful "
> I want to know position and location of drug molecules relative to the DPPC
> bilayer during simulation time.
> In your opinion, how should I use this tool (g_traj)?

I wouldn't.  You can extract the needed information with a couple of steps of 
post-processing, but it's not worth it when g_dist will do this with no extra 

> Is g_dist appropriate for obtaining distance between center of mass of the
> drug molecules and DPPC lipid bilayer as a function of simulation time?

Yes, use g_dist.  But the x- and y- components aren't useful, so the (absolute 
value of) the z-component of the distance is what you need.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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