[gmx-users] Getting out of the box!!!

[Marcelo Fabricio Masman]

Thank you very much for your recommendations, Tsjerk.

Marcelo


On 5/10/06, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
> Marcelo,
>
> Have you considered reading the FAQ, searching the mailing list, reading
> the manual or just paying attention? Just yesterday there was mention of a
> ligand jumping out of the box, to which several replies were given and your
> exact question is asked on this list at least every month!
>
> I'll keep my temper. It's just due to the periodic boundary conditions,
> nothing wrong, you can use trjconv with option -pbc nojump afterwards or you
> can set comm_mode to linear with the protein as comm_group. Now please read
> the manual on periodic boundary conditions and for further reference search
> the mail list (e.g. "periodic boundary conditions", "PBC", "jumping",
> etc...)
>
> Tsjerk
>
>  On 5/10/06, Marcelo Fabricio Masman <mmasman at gmail.com> wrote:
>
> >  Hello gmx users:
>
> I am running a very common MD simulation and the protein system is getting
> OUT of the box after approximately 200 ps. I have tried several things.
> Does it happen very frequently? (common mistake)
> Is there any way to keep, during the whole calculation, the protein system
> into the center of the box?
> What could I do for avoiding this phenomenon?
>
> Thanks in advance.
>
> Marcelo
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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
>
>
>
>
> --
>
> Tsjerk A. Wassenaar, M.Sc.
> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747AG Groningen, The Netherlands
> +31 50 363 4336
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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/20060510/dfe2e645/attachment.html>