[gmx-users] Re: editconf -d

[David van der Spoel]

Isabella Daidone wrote:
> Hi,
> 
> this is what is written in one of the options in editconf:
> " -[no]c   bool     no  Center molecule in box (implied by -box and -d)".
> Moreover, in the mailing list you can find discussion about this topic 
> with version 3.2 and David said it was a bug (that -d -c did not really 
> center).
> So I was simply wondering if the bug was corrected or if I am missing 
> something else.
> 

Just checked the code, I don't see why it shouldn't work as adevertised. 
Please submit a bugzilla with example inputs.


> Cheers.
> 
> Isabella
> 
> On Thu, 20 Jul 2006, X.Periole wrote:
> 
>>
>> HI Isabelle,
>>
>>
>>> I try again, just to know if it is not true that -d implies centering...
>>>
>>>> Hi,
>>>>
>>>> when using editconf -d with gromacs version 3.3, it seems that the 
>>>> protein is not at the center but at the corner of the box.
>>>> In gromacs version 3.3, does option -d in editconf really imply that 
>>>> the protein will be centered or is there still a bug (as in version 
>>>> 3.2.1) or am I missing something?
>>
>>
>> I don't think the -d option, which defines the minimum
>> distance to the edge of the box, centers the protein into
>> the box. You would have to use -c to center the protein and
>> -d to define the size of your box !
>> Why would that be a bug ?
>>
>> Best
>> XAvier
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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