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

Justin Lemkul jalemkul at vt.edu
Fri Aug 2 02:06:40 CEST 2013

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 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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