[gmx-users] solvation

[Jamie Seyed]

Hi Justin,
Thanks for your answer,
On Thu, Aug 13, 2009 at 11:42 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Jamie Seyed wrote:
>
>> Dear all,
>> 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
>>
>
> (1) The -vdwd option may help, or even -ci -nmol.  If you have a pore,
> wouldn't water diffuse in over time anyway during equilibration (assuming an
> otherwise correct setup and realistic physical model)?


Long time ago I did an experiment on water in confined geometry and I want
to see if the results can obtain from the  simulation... So for using -nmol
-ci (at random position), it says I must use a file like insert.gro would
you please explain me how I can make insert.gro?

>
> (2) If you haven't re-positioned your system within the box, it probably
> doesn't make any sense.  The Gromacs convention is to place the corner of
> the box at the coordinate origin, and everything else is relative to that.
>  Is a 1-nm cubic box large enough to encompass your system?  If not, genbox
> is doing what it's told - filling a 1-nm box near the origin, and leaving
> everything else out.


>
> -Justin
>
>  changing the box size will give a opposite result. Please advise..Thanks
>> in advance/Jamie
>>
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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