[gmx-users] Periodic boundary problem

Berk Hess gmx3 at hotmail.com
Thu Nov 4 11:20:46 CET 2004

>From: "Haberl Florian" <Florian.Haberl at chemie.uni-erlangen.de>
>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] Periodic boundary problem
>Date: Thu, 4 Nov 2004 11:03:38 +0100 (CET)
> > did you try trjconv -pbc cluster?
>Handbook on page 311 says:
>- cluster ... only meaningful results if you in fact have a cluster, but i
>don^t think i^ve got an cluster, its only a dimer proteine.
>I tried same trjconv command (same in/output parameters) with cluster
>instead of jump
>Fatal error: calloc for bMol (nelem=-1073748280, elsize=4, file trjconv.c,
>line 84): Cannot allocate memory
>is the result.
>Anyone tried the cvs version with fixed trjconv (
>http://www.gromacs.org/pipermail/gmx-revision/2004-October/000036.html )

I made this fix.
It only applies to the combination -pbc nojump with -fit rot+trans or 

trjconv -s -pbc nojump
should fix the problem when the tpr file given with -s has the correct 
complex conformation.

Note that your problem is not really a problem, unless you want to make nice 
or do a visual inspection.


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