[gmx-users] solvation

[Justin A. Lemkul]

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

The "insert.gro" file contains the coordinates of one molecule that you want to 
insert, i.e. one water molecule.

-Justin

>     (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 <http://vt.edu/> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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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

========================================