Dear all,
sorry I forgot -Sg option, now it works
g_order_d -e 2000 -n index-ow.ndx -Sg
By the way I realized that in this way I have only the average of the
tetrahedral order parameter inside the group.
Is there any possibilities to have the order parameter associated to
each oxygen inside the group?
Thank you again
Ivan
On 05/05/2011 02:33 PM, Ivan Gladich wrote:
Dear all
I am simulating a water slab using a 6-site water model and I would
like, for each time step, to calculate the tetrahedrality order
parameter of every water oxygens using the four nearest neighbour
Oxygens.
From g_order documentation I read that this is possible with g_order
command
"The tetrahedrality order parameters can be determined around an atom.
Both
angle an distance order parameters are calculated. See P.-L. Chau and
A.J.
Hardwick, Mol. Phys., 93, (1998), 511-518. for more details."
So I created an index.ndx file that contains the oxygen atom [OW]
using make_ndx.
After that, as suggested by the manual,
http://manual.gromacs.org/current/online/g_order.html
I removed all the groups expected the [OW] and I created a new index
index-ow.ndx
Then I used the command g_order
g_order_d -e 2000 -n index-ow.ndx -nr index-ow.ndx -d y -permolecule
I obtain the following output
####################################3
....
Taking y axis as normal to the membrane
Reading file topol.tpr, VERSION 4.5.4 (double precision)
Calculating Scd order parameters for each of 2880 molecules
Using following groups:
Groupname: OW First atomname: OW First atomnr 0
Reading frame 0 time 0.000 Number of elements in first
group: 2880
Calculating order parameters for each of 2880 molecules
Last frame 2000 time 2000.000
Read trajectory. Printing parameters to file
Back Off! I just backed up order.xvg to ./#order.xvg.3#
Back Off! I just backed up sliced.xvg to ./#sliced.xvg.3#
gcq#260: "I Quit My Job Blowing Leaves" (Beck)
#######################################
By the way, if I look the file order.xvg, it is empty
Did I miss something? I searched in the web for some hint without
success...
thank you for any help,
Ivan
--
------
Ivan Gladich, Ph.D.
Postdoctoral Fellow
Academy of Sciences of the Czech Republic
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
Flemingovo nám. 2.
166 10 Praha 6
Czech Republic
Tel: +420775504164
e-mail: ivan.glad...@uochb.cas.cz
web page:http://www.molecular.cz/~gladich/
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