[gmx-users] non-zero potential in pure POPC bilayer Odd profile across bilayer

[himanshu khandelia]

No, the membrane is between the two "2" numerals.

With 3-4 ns equilibration, the total potential difference between the
two sides of the membrane should be zero, and the potential should be
continuous at the box edges. So there is some other problem

On Dec 3, 2007 7:39 PM, Pedro Alexandre de Araújo Gomes Lapido
Loureiro <palaplou at gmail.com> wrote:
> 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 <hkhandelia at gmail.com>:
> >
> >
> >
> > 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
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