[gmx-users] -shell in genbox

[David van der Spoel]

On Thu, 2002-09-26 at 11:30, Dmitry Kovalsky wrote:
> Hi there
> can anybody explain the sence of an option -shell in genbox programm
> Wether I use it or not I get finally the same number of water molecules 
> I mean
> #genbox  -cp prot_b4genbox_shell.gro -cs -o prot_b4em -p prot
> 
> or 
> 
> #genbox -cp prot_b4genbox_shell.gro -cs -o prot_b4genbox -p prot -shell 0.15
> #genbox -cp prot_b4genbox.gro -cs -o prot_b4em -p prot
> 
> I get the same overall number of water molecules.
And the same conformation too? (i.e. the same waters)?
> 
> I also noticed when the -princ option in editconf is used, the following 
> genbox with -shell option resulted in 0 water molecules.
0.15 will probably not give you any waters. To make it work you'd want
to center your molecule in  a box
editconf -f prot.gro -c -d 1 o b4genbox
genbox -cp b4genbox -cs -shell 0.4
should give you a shell of 0.4 nm water.



> 
> Thanks in advance
> -- 
> Sincerely yours,
> 
> Dima
> 
> Ph.D. Student Dmitry Kovalsky
> Institute of Molecular Biology & Genetics
> 150 Akad. Zabolotnogo Street,
> Kiev-143, 03143
> UKRAINE
> 
> E-mail: dikov at imbg.org.ua
> Fax:  +380 (44) 266-0759
> Tel.: +380 (44) 266-5589
> 
> 
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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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