Jamie Seyed wrote:
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.
Right, like I said before, the insert.gro file should contain coordinates for
*one* molecule.
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
Well, how did you make this file? A .gro file has a specific format:
http://manual.gromacs.org/current/online/gro.html
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
I have no idea how you created this broken file, so I can't really comment :)
The easiest thing to do (I would think) would be to take the first molecule of
spc216.gro, keep the header lines, set number of atoms = 3 and preserve the box
information at the bottom. I've used that before in a few cases.
-Justin
On Thu, Aug 13, 2009 at 1:20 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
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]>
<mailto:[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/> <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 <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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