[gmx-users] solvation

[Jamie Seyed]

Hi Justin,
I made an insert.gro file for 2 water molecules,  and when I used genbox I
got a fatal error: more than one residue in insert molecules, program
terminated.
I wanted to look at insert.gro, it does not show anything. And when I
convert it to pdb I got a warning [file aminoacids.dat, line 1]: Bad box
file insert.gro
When I looked at the insert.pdb file I found only 1.5 water molecule! Which
means 1 water plus a OH. Do you have any idea what should I do or if I am
missing some thing? Many Thanks in Advance/Jamie

On Thu, Aug 13, 2009 at 1:20 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ========================================
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