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
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