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

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

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

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