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) <[EMAIL PROTECTED]> 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: [EMAIL PROTECTED] 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
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