[gmx-users] protein goes out from the waterbox during MD

[Pedro Alexandre de Araújo Gomes Lapido Loureiro]

Eugenia,

this is only a visualization issue. Try  the options -pbc nojump/whole/inbox
in trjconv.

Regarding comm_mode, I think you should use linear.

Regards,

Pedro.

2007/1/30, Eugenia Polverini <eugenia.polverini at fis.unipr.it>:
>
> Dear all,
> in the output of my 5 ns MD of a small protein in a box of water and
> pbc, I see that during MD the protein goes out from the box.
> Why it happened? Is it a problem or I can accept that all was OK?
> I have set the comm_mode=angular.
>
> Thanks for your help!
> Best regards
> Eugenia
>
>
>
> --
> Eugenia Polverini, Ph.D.
> Dept. of Physics
> University of Parma
> Parco Area delle Scienze, 7/A
> 43100 Parma
> ITALY
>
> Phone: +39 0521 905254
> Fax: +39 0521 905223
> E-Mail: eugenia.polverini at fis.unipr.it
> http://www.fis.unipr.it/~polveri
>
>
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