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
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
==================================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
