[gmx-users] g_potential and trjconv: problems with bilayer simulation analysis

Justin Lemkul jalemkul at vt.edu
Fri Aug 2 16:35:26 CEST 2013

On 8/2/13 10:33 AM, wood irene wrote:
> Hello
> thanks for the answer
> I've tried this option, but the obtained result is the g_potential with the
> popc profile plotted from 0 to 7nm, being one monolayer from 0 to 3.5,
> region corresponding to "water" phase at z=3.5 and the other one monolayer
> from 3.5 to 7. In fact lipid bilayer core is at z=0. The profile present a
> drift, possibly due to fluctuations in the z (by pressure coupling) and the
> differences in water density at any side of lipid bilayer. I'm looking in a
> Gurtovenko's article (J.Chem.Phys 130, 215107 (2009)) a similar artifact
> regarding time dependence of bilayer electrostatic potential and the drift
> origin due to bilayer COM fluctuation during simulation. In this paper the
> authors suggest to center the positions of all the systems atoms with
> respect to the bilayer COM in each frame.
> So, is possible to obtain a similar profile, with trjconv tool or any
> other, but starting at -3.5 to 3.5, with the whole bilayer centered at z=0?
> Or this result is obtained by mathematic transformation?

Gromacs, by default, builds periodic boxes in the positive (x,y,z) dimensions, 
so no tool will ever report a negative box vector.  This is a simple 
mathematical transformation, or even simpler, just altering the values of the 
axis, because what you're plotting is exactly what you want.



Justin A. Lemkul, Ph.D.
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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