[gmx-users] center of mass motion

[Tsjerk Wassenaar]

Dear Anna,

The option you want for trjconv is -pbc nojump
This will remove jumps over the periodic boundaries. Alternatively you can
fit to a reference group, to keep the protein in a fixed position /
orientation (-fit rot+trans). Please also check the help of trjconv (trjconv
-h).

Tsjerk

On 1/4/06, herbst at fhi-berlin.mpg.de <herbst at fhi-berlin.mpg.de> wrote:
>
> trjconv does not know this option
>
> > use trjconv -center tric -f in.xtc -o out.xtc
> >
> > Yang Ye
> > Nanyang Technolgoical University, Singapore
> >
> > ----- Original Message ----
> > From: Florian Haberl <Florian.Haberl at chemie.uni-erlangen.de>
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Sent: Wednesday, January 04, 2006 7:16:40 PM
> > Subject: Re: [gmx-users] center of mass motion
> >
> > hi
> >
> > On Wednesday 04 January 2006 11:22, herbst at fhi-berlin.mpg.de wrote:
> >> Hi all,
> >>
> >> my protein is jumping out of the box during the simulation. I tried to
> >> center it in the box using trjconv -pbc inbox -center, but when I look
> >> at
> >> the new trajectory, it is still leaving the box and I can't watch it.
> >> Am I doing something wrong ?
> > Take a reference strucuture which is inside the box, normally the
> > minimized em
> > or pr file. ( trjconv -s file. ...)
> >
> >
> >> And how can I constrain the center of mass motion in the simulation ?
> >
> >
> >
> >>
> >> Thanks,
> >> Anna
> >> _______________________________________________
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> >
> > Greetings,
> >
> > Florian
> >
> > --
> >
> -------------------------------------------------------------------------------
> >  Florian Haberl
> >  Computer-Chemie-Centrum
> >  Universitaet Erlangen/ Nuernberg
> >  Naegelsbachstr 25
> >  D-91052 Erlangen
> >  Mailto: florian.haberl AT chemie.uni-erlangen.de
> >
> -------------------------------------------------------------------------------
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> >
> >
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>



--

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
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