[gmx-users] PBC problem

Andrea Carotti and.carotti at farmchim.uniba.it
Mon Jul 19 12:23:51 CEST 2004

Thanks Berk for the suggestion,
    I've done the double step: pbc nojump and then -fit rot+trans and
everything worked fine.

----- Original Message ----- 
From: "Berk Hess" <gmx3 at hotmail.com>
To: <gmx-users at gromacs.org>
Sent: Monday, July 12, 2004 5:11 PM
Subject: Re: [gmx-users] PBC problem

> >From: "Andrea Carotti" <and.carotti at farmchim.uniba.it>
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> >Subject: Re: [gmx-users] PBC problem
> >Date: Mon, 12 Jul 2004 16:12:35 +0200
> >
> >I'm using
> >trjconv -f traj.trr -s file_MD.tpr -fit -o traj_fitted.trr -n index.ndx
> >but I'm still having the error message invalid argument -o for
> >option -fit...
> >(probably silly but I've also tried to use as argument for fit:
> >Ref_struct.gro and file_MD.tpr)
> trjconv -h
> tells you what you should put after the -fit option.
> Unfortunately the person who changed this option from a boolean to an enum
> has not updated the description, but the options list also gives the
> options.
> I guess you would want to use -fit trans
> But I think this will not solve problem, as the second chain can then
> jump out of the box.
> The problem is that the centering is done first and the pbc correction
> that.
> So I would suggest running trjconv twice.
> First trjconv -pbc nojump
> And then trjconv -center
> Berk.
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