[gmx-users] PBC problem

[Berk Hess]

>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 still
jump out of the box.

The problem is that the centering is done first and the pbc correction after 
that.
So I would suggest running trjconv twice.
First trjconv -pbc nojump
And then trjconv -center

Berk.

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