[gmx-users] PBC problem in bilayer system

[Justin Lemkul]

On 9/15/14 12:11 PM, shahab shariati wrote:
> Dear Justin
>
> Very very thanks for your time and consideration.
>
> Excuse me for many questions.
>
> I want to make sure my trajectory is valid and accurate for analysis and
> then for writing related paper.
>

It is.

> My last question is that can I use this trajectory for doing analysis such
> as
>
> g_traj, g_dist, g_density, g_rdf, g_order, g_msd, g_hbond .............?
>

Sure.  Gromacs tools handle PBC effects just fine.  You're getting hung up on 
something that's simply measured crudely.  The absolute z-coordinate in this 
case means very little, precisely for the reasons we've been saying.  The 
difference in z-coordinate between the drug molecules and the bilayer, provided 
that it is measured consistently, is a much more informative metric, assuming 
you're using it to indicate binding events.  The raw output of g_traj in this 
case is not very useful.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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