[gmx-users] jumps through the box

[Rainer Boeckmann]

Dmitry Kovalsky wrote:

> Hi
>
> My protein consists of two chains and when I perform long simulation and it
> moves toward box edge one subunit begans jumping.
>
>  I have tried like  here was suggested
> http://www.gromacs.org/pipermail/gmx-users/2002-June/001899.html
> This helps but only in part: the two monomers are "reconnected" but now the
> whole protein jumps.
>

after the trjconv -whole you should apply trjconv -nojump. that will keep the
molecule whole AND remove jumps.



>
> Is there a full desision of the problem?
>
> --
> Sincerely yours,
>
> Ph.D. Student Dmitry Kovalsky
> Institute of Molecular Biology & Genetics
> 150 Akad. Zabolotnogo Street,
> Kiev-143, 03143
> UKRAINE
>
> E-mail: dikov at imbg.org.ua
> Fax:  +380 (44) 266-0759
> Tel.: +380 (44) 266-5589
>
> _______________________________________________
> 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.

--
Rainer Böckmann
Theoretical Molecular Biophysics Group
Max-Planck-Institute for Biophysical Chemistry
Am Faßberg 11
D-37077 Göttingen

Tel.: +49(551)201-1141, Fax.: +49(551)201-1089
email: rboeckm at gwdg.de

http://www.mpibpc.gwdg.de/abteilungen/071/rainer/index.html