[gmx-users] genbox

David van der Spoel spoel at xray.bmc.uu.se
Wed May 1 18:45:23 CEST 2002

On Wed, 1 May 2002, Pedro Alexandre de Araujo Gomes Lapido Loureiro wrote:

>No. In fact, I am solvating a peptide (out.gro) in a box with water and TFE
>With the option -ci, I am using only one molecule because the manual (pg. 216)
>says so.
>The command line is:
>genbox -cp out.gro -ci tfe.gro -o mshtfe1.gro

But if either out.gro or tfe.gro already contains water it's not going to
You want to first add some tfe to your peptide (is your box big enough?
check last line in out.gro) and then add water.

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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