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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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