[gmx-users] Re: editconf -d

Isabella Daidone i.daidone at caspur.it
Thu Jul 20 10:24:25 CEST 2006


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 
So I was simply wondering if the bug was corrected or if I am missing 
something else.



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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