[gmx-users] solvation of protein

Haberl Florian Florian.Haberl at chemie.uni-erlangen.de
Sun Jul 16 13:55:58 CEST 2006


> Hi
> when i am trying to solvate my protein in water box, i am not getting my
> protein in the center of but at one face of water box with some atoms
> outside waterbox. what should i do for this problem? should i move center
> of my protein to the center of water box using some tcl script in vmd?
> how can i include the crystallographic water in the *.gro file for
> simulation?

Use option -c for center in editconf it is also useful to add here
distance to box end

editconf -c -d 0.8

or something like this.

> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php



 Florian Haberl              Universitaet Erlangen/Nuernberg
 Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen

 Mailto: florian.haberl AT chemie.uni-erlangen.de


More information about the gromacs.org_gmx-users mailing list