[gmx-users] solvation of protein

[Tsjerk Wassenaar]

Hi Dhiraj,

Your truncated octahedron box is represented as a rectangular unit
cell (check the manual) and I think that the center, given your
command line, means center of the truncated octahedron. But it doesn't
matter whatsoever. In the infinite simulation system there is no cell
and definitely no center. By the way, wouldn't you rather use a -bt
dodecahedron ? cuts further on the size of the system and is less
likely to give an effect on the simulation itself.

Tsjerk

On 7/16/06, Srivastava, Dhiraj (UMC-Student) <dshv6 at mizzou.edu> wrote:
> I am using the following commandfor solvating my protein but i am stiil getting my protein at one face of box.
>
> editconf -bt octahedron -f trp2.pdb -o trp2.pdb -c -d 0.6
>
>
> ________________________________
>
> From: gmx-users-bounces at gromacs.org on behalf of Haberl Florian
> Sent: Sun 7/16/2006 6:55 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] solvation of protein
>
>
>
> Hi,
>
> > 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.
>
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>
> greetings,
>
> Florian
>
> ------------------------------------------------------------------------
>  Florian Haberl              Universitaet Erlangen/Nuernberg
>  Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen
>
>  Mailto: florian.haberl AT chemie.uni-erlangen.de
>
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-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336