[gmx-users] Re: solvation

Vitaly V. Chaban vvchaban at gmail.com
Thu Aug 13 20:10:55 CEST 2009

What is the box size and what is the cutoff displayed by genbox?

On Thu, Aug 13, 2009 at 8:10 PM, Jamie Seyed<jamie.seyed at gmail.com> wrote:
> 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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