[gmx-users] Periodic boundary problem

Haberl Florian Florian.Haberl at chemie.uni-erlangen.de
Thu Nov 4 14:11:22 CET 2004

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

So i only need to take an input file with the "correct" look (both dimers
together), and then it should work?

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

So how can i fix it, if i want to make nice pictures or animations?

> Berk



 Florian Haberl              Universitaet Erlangen/Nuernberg
 Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen

 Mailto: florian.haberl AT chemie.uni-erlangen.de


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