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

wood irene irewood at gmail.com
Fri Aug 2 00:55:32 CEST 2013

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.
I will be very grateful with any advice,
Thanks in advance


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