[gmx-users] Periodic boundary problem

[Kay Gottschalk]

I had a dimer and it worked fine with trjconv -pbc cluster -n, using   
protein ('1') for clustering.
K.

On Nov 4, 2004, at 12:03 PM, Haberl Florian wrote:

>
>> 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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>>>
>> Dr. Kay-E. Gottschalk
>> Department of Biological Chemistry
>> Weizmann Institute of Science
>> Herzl St. 1
>> Rehovot
>> Israel
>> +972-8-934 3639
>>
>> _______________________________________________
>
>
>
> ----------------------------------------------------------------------- 
> -
>  Florian Haberl              Universitaet Erlangen/Nuernberg
>  Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen
>
>  Mailto: florian.haberl AT chemie.uni-erlangen.de
>
> ----------------------------------------------------------------------- 
> -
> _______________________________________________
> gmx-users mailing list
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>
Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Herzl St. 1
Rehovot
Israel
+972-8-934 3639