[gmx-users] Re: -shell in genbox
dikov at imbg.org.ua
Sat Sep 28 15:07:25 CEST 2002
On Saturday 28 September 2002 07:33, gmx-users-request at gromacs.org wrote:
> 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 rechecked surrounding protein water molecules and they ahve the same
positions in both cases.
> > 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
I did the same but without -c option bacause in grompp online manual I read
"Center molecule in box (implied by -box and -d)"
> genbox -cp b4genbox -cs -shell 0.4
> should give you a shell of 0.4 nm water.
May be I should try your value...
Ph.D. Student Dmitry Kovalsky
Institute of Molecular Biology & Genetics
150 Akad. Zabolotnogo Street,
E-mail: dikov at imbg.org.ua
Fax: +380 (44) 266-0759
Tel.: +380 (44) 266-5589
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