[gmx-users] g_order for water

[Ivan Gladich]

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.gladich at uochb.cas.cz
web page:http://www.molecular.cz/~gladich/
-----