[gmx-users] editconf

SANTINI sebastien sebastien.santini at igs.cnrs-mrs.fr
Fri Jan 23 16:21:01 CET 2004

Hi all,

I had a problem.
I have found an answer but maybe someone have the same problem ...

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



Sebastien SANTINI, PhD Student
sebastien.santini at igs.cnrs-mrs.fr
Tel:   +33 4 91 16 44 55                Fax:   +33 4 91 16 45 49
Laboratory of Structural & Genomic Information (IGS), UPR2589 - CNRS
Institute of Structural Biology & Microbiology (IBSM)
31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, FRANCE

More information about the gromacs.org_gmx-users mailing list