[gmx-users] periodicity and correct output

[Shuangxing Dai]

Yes, mdrun applies PBC at every step and some atoms at top/bottom will
translate to the bottom/top at some steps. So in dynamics simulation, the
polarization given by gromacs is meaningless. Is there anyway I can apply
PBC without translation ( e.g. change the box center automatically to avoid
translation) ?
Thanks,
Shuangxing Dai


On Wed, Jul 28, 2010 at 11:46 AM, Vitaly Chaban <vvchaban at gmail.com> wrote:

> Hi Shuangxing,
>
> For my case, I wrote a script just to do +/- LBOX when x>LBOX || x <
> 0. I am not well familiar with polarization algorithm in gromacs but
> it seems not to be a problem during a run since mdrun applies PBC at
> every step. Maybe I am false here...
>
> Vitaly
>
>
> On Wed, Jul 28, 2010 at 6:35 PM, Shuangxing Dai <shuangxingdai at gmail.com>
> wrote:
> > I think I met the same problem. When apply periodicity to the system,
> some
> > atoms will translate to the other side of the box, and this gives wrong
> > polarization values (especially in dynamic simulations). Anyone has idea
> how
> > to prevent this and get correct polarization in dynamics?
> > Thanks,
> > Shuangxing Dai
> >
> >
> > On Mon, Jul 26, 2010 at 12:26 AM, Vitaly Chaban <vvchaban at gmail.com>
> wrote:
> >>
> >> Hi,
> >>
> >> Is there an option in any gromacs utility to apply periodicity to the
> >> output configuration or trajectory? I want to get all the coordinates
> >> just within an elementary box, between 0 and LBOX in spite of any
> >> details of the system.
> >>
> >> For example, "editconf -no(pbc)" does not do its work since after
> >> processing negative coordinates are sometimes present as well as those
> >> bigger than LBOX.
> >>
> >> Vitaly
> >>
> >> Dr. Vitaly Chaban
> >> --
> >> gmx-users mailing list    gmx-users at gromacs.org
> >> http://lists.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 gmx-users-request at gromacs.org.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100728/70b9675b/attachment.html>