If I understood your graph correctly, the "valleys" represent the contribution from the headgroups and the central "peak" lies in the middle of the bilayer. It can be seen that the two monolayers are not equivalent which is probably due to lack of equilibration. You can convince yourself by measuring the density of the system along the axis normal to the bilayer (use g_density -h).
Regards. Pedro. 2007/12/3, himanshu khandelia <[EMAIL PROTECTED]>: > > Hi, > > I calculated the electrostatic potential using g_potential across a > large 416-lipid POPC bilayer from a 200 ps trajectory. The bilayer is > well-hydrated, and has zero charge. > > However, I get a very odd potential which starts off at 0.0 and ends > at 0.6 V, but is not monotonically increasing all the time. I can > attach a small 8 kb jpg if the admins allow it. Otherwise you might > get an idea of the shape from the diagram below if it turns up right. > The bilayer is between the points 2 and 2. Any tips why this might > happen ? > > Thank you very much ! > > -Himanshu > > > > 1 > 1 > 1 > 1 > 1 > 1 > 1 > 1 1 > 1 1 1 > 1 1 1 > 1 1 1 > 1 1 2 > 1 1 1 1 > 1 1 1 1 > 1 1 1 > 1 1 > 2 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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