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? Thank you
2013/8/1 Justin Lemkul <jalem...@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 > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) 706-7441 > > ==============================**==================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- *Ire* -- 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
