[gmx-users] Re: editconf -d
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jul 20 10:36:14 CEST 2006
Isabella Daidone wrote:
> 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.
Just checked the code, I don't see why it shouldn't work as adevertised.
Please submit a bugzilla with example inputs.
> 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...
>>>> 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 ?
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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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