[gmx-users] simulation box

[David van der Spoel]

On Wed, 24 Apr 2002, Nguyen Hoang Phuong wrote:

>
>
>Hi,
>thank you very much. I have done as the following:
>
>I  solvate my peptide in the default spc216.gro water with the
>desired box size (using the option -box in the editconf and genbox). Then
>I delete some water molecules in the gro file to get the desired number 
>and change the number SOL in the top file. How do you think about this
>way? Thank you.
this is also what I usually do. By modifying the box size, one can get 
quite close usually. Then use some pressure coupling to make it 
homogeneous density.

-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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