[gmx-users] Re: solvation

Jamie Seyed jamie.seyed at gmail.com
Thu Aug 13 19:10:16 CEST 2009

Hi Vitaly,
Thanks for the answer. When I said far away means my pore was in one corner
of vmd window and the water molecules in opposite corner (almost). Anyways,
I tried to use your method but I think I am missing some parts...
I did:
(1)editconf -bt cubic -f conf.gro -o pore_edco.pdb -d 0.02  ---> seems fine
(2)genbox -cp pore_edco.pdb -cs spc216.gro -o pore edco_b4em.pdb -p
topol.top  here there is an error: one of the box vectors has become shorter
than twice the cut-off length or box_yy-|box_zy| or box_zz has become
smaller than the cut-off.

would you please let me know how I can fix the error (I don't see where I
can change the cut-off !). Also am I doing right or I need a box of water
first without introducing my molecule...
I appreciate to get more information and some help... Thanks a lot/Jamie

On Thu, Aug 13, 2009 at 12:21 PM, Vitaly V. Chaban <vvchaban at gmail.com>wrote:

> Jamie,
> I didn't understand why you meant saying "waters far from the outside
> of the pore"... Far from outside, then where exactly? Maybe I just
> imagine your box incorrectly.
> To fill the pore with a solvent try to "deceive" genbox a little:
> 1) make a box (see editconf) in such a way that it contains only
> "inside" part of your pore. genbox will not report an error from its
> side.
> 2) add the solvent with genbox.
> 3) return to the original box size.
> 4) add the outside part.
> Vitaly
> > I want to know how can I use genbox to fill inside of the pore as well as
> a
> > layer outside. From the "man genbox" page I try to use -shell with a
> > negative value (?) but it put waters far from the outside of the pore and
> I
> > think it does not care about the sign. It seems strange to me because
> when I
> > had 10 10 10 in the last line of my f.gro, by a shell 0.5 or 0.2, I got a
> > layer of few molecule around the pore, but when I change it to 1. 1. 1.,
> the
> > water molecules generated far away. I appreciate if someone tell me (1)
> how
> > I can add water inside the pore and (2) why changing the box size will
> give
>  > a opposite result. Please advise..Thanks in advance/Jamie
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