jamie.seyed at gmail.com
Thu Aug 13 18:00:38 CEST 2009
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.
> 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
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