[gmx-users] Periodic boundary problem

[Haberl Florian]

> 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 )

any suggests ?


Greetings,

Florian

>
> On Nov 4, 2004, at 11:14 AM, Haberl Florian wrote:
>
>> dear gmx-users,
>>
>> I want to perform an md simulation with an dimer proteine.
>> after performing em/pr/ or md the dimer is seperated in
>> two monomers and one of this is outside my waterbox
>> (viewed by gopenmol).
>>
>> After some search i found the trjconv command should fix this
>> problem which is caused through periodic boundary conditions
>> (i guess this is the problem).
>>
>> So an -pbc nojump should fix it, but this is not always so,
>> sometimes it^s still outside the box and i don^t know why.
>>
>> Tried this now with several input files but always same behavoir.
>>
>> Any suggests how to fix this?
>>
>>
>> Greetings,
>>
>> Florian
>>
>>
>> -----------------------------------------------------------------------
>> -
>>  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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> _______________________________________________



------------------------------------------------------------------------
 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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