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/
-----
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
