[gmx-users] editconf ver. 3.2.

[David]

On Mon, 2004-02-16 at 21:59, Tivadar Orban wrote:
> Hi,
> 
> I am using Gromacs ver 3.2 and when after pdb2gmx  I run
> editconf ­ff oplsaa¹ -f in.gro -o out.gro -c -d 0.5
> Followed by
> genbox -cp out.gro -cs tip4p.gro  -o em.gro -p out.top
> 
> Somehow even though I set -c to center my peptide, is out of the water box.
> This is before doing any EM or MD.
> 
> I tried the same thing in ver 3.1.4 and no problem there (the peptide is in
> the center of the box).
> 
> Any idea why?
A bug.

Use the -center option.
> 
> Regards,
> Tivadar Orban
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel
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