[gmx-users] editconf

[David]

On Fri, 2004-01-23 at 16:26, SANTINI sebastien wrote:
> Hi all,
> 
> I had a problem.
> I have found an answer but maybe someone have the same problem ...
> 
> using
> editconf -f PROT.gro -o PROT.box.gro -bt dodecahedron -box 8.2 -density 1000
> 
> the rmsd between PROT.gro and PROT.box.gro is bigger than 0.4 nm
> 
> i didn't understood why the rmsd was so big.
> 
> i've tried to change some options and finaly remove "-density 1000"
> 
> then with exactly the same command line (and a the default density) 
> 
> the rmsd has became smaller than 0.01 nm
> 
> So, if you just need to use a density of 1000 g/l i think it's better to
> use the default and remove -density 1000
The density command scales the whole box, so probabably your protein has
been stretched. It is a feature, not a bug...

> 
> 
> SEB.
-- 
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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