[gmx-users] g_order for water

Ivan Gladich ivan.gladich at marge.uochb.cas.cz
Thu May 5 15:37:51 CEST 2011


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




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