[gmx-users] PBC problem

[Andrea Carotti]

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

----- 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
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.
>
> _________________________________________________________________
> Play online games with your friends with MSN Messenger
> http://messenger.msn.nl/
>
> _______________________________________________
> 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.
>