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

wood irene irewood at gmail.com
Fri Aug 2 16:33:05 CEST 2013

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?
Thank you

2013/8/1 Justin Lemkul <jalemkul at vt.edu>

> On 8/1/13 6:55 PM, wood irene wrote:
>> Hi all
>> I'm trying to calculate the electrostatic potential of POPC membrane
>> systems from a trajectory.
>> When I use g_potential, the calculation is well done but the results are
>> plotted from 0 to 7 nm of Z coordinates, with the bilayer center near to
>> 3.5nm. Is possible, modifying the trajectory in order to obtain the
>> results
>> centered in Z=0nm for my membrane simulation? Wich are the steps that I
>> need to follow?
>> I have tried using trjconv but I can not achieve any good solution, with
>> the system centered in bilayer core at z=0. I think that may be using a
>> combination of boxcenter/center, pbc and trans I could resolve it, but I'm
>> not familiar with the correct steps.
> trjconv -center (centering on POPC) followed by trjconv -trans 0 0 -3.5
> -pbc mol should get you pretty close, though if you're using pressure
> coupling, that 7-nm z-dimension is not fixed so you may need to tweak the
> translation distance.
> -Justin
> --
> ==============================**====================
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
> Department of Pharmaceutical Sciences
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> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> ==============================**====================
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