[gmx-users] non squares box

[Tsjerk Wassenaar]

Right, there was no reference whatsoever to MD. The first sentence,
preluding the problem, mentioned editconf. The second, mentioned
trjconv. No grompp/mdrun etc in between. Anyway, also to check the
periodicity in your output (note how flexibly I adapt it to the
current situation):

genconf -f confout.gro -o out.pdb -nbox 2 2 2

:p

Tsjerk

On Sun, Jun 21, 2009 at 1:33 PM, Mark Abraham<Mark.Abraham at anu.edu.au> wrote:
> Omer Markovitch wrote:
>>
>> Thanks.
>> I am not sure how this addresses my problem. I am getting "broken"
>> structure at the end of the MD (in confout.gro),
>
> Well, you didn't say you were doing MD. I (and presumably Tsjerk) thought
> you were converting your output from editconf. In such a case, Tserk's
> suggestion lets you tile some boxes together to see how things are (not)
> working. Your results will also depend on the contents of your editconf -f
> file.gro. I suggest you copy and paste your actual commands in future :-)
>
> Mark
>
>> and want to be sure that GMX treat it correctly during the MD.
>>
>>    To check your periodicity use genconf:
>>
>>    genconf -f in.pdb -o out.pdb -nbox 2 2 2
>>
>>
>>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623