[gmx-users] simulation box

David van der Spoel spoel at xray.bmc.uu.se
Thu Apr 25 05:26:30 CEST 2002

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

>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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