[gmx-users] simulation box

David van der Spoel spoel at xray.bmc.uu.se
Thu Apr 25 04:59:30 CEST 2002

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

>Dear All,
>Does anyone know how to create the simulation box which contains peptide
>and water at the given box size and the number of water molecules? What I
>have done is that I specify the density (corresponding to the voluum and 
>the number of water molecules) in the program editconf but when I use the
>program genbox, he gives me default value of the density. Thanks for your
>help in advance.
You can put the peptide in a box of your wanted size (with editconf) and 
then use genbox to insert water. You can not have both exact number of 
waters and box size in genbox, but you can tune either by modifying the 
box size.

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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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