Jamie Seyed wrote:
Hi Justin,
Thanks for your answer,
On Thu, Aug 13, 2009 at 11:42 AM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> 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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