[gmx-users] order parameter for UAFF model

[Justin A. Lemkul]

afsaneh maleki wrote:
> thanks for your reply
> 
> i have got output file,i used the following options:
> # g_order -f md.xtc -s md.tpr  -n sn1.ndx   -o order-sn1.xvg   -od 
> deuter-sn1.xvg    -d z
> 
> whatever deuter-sn1.xvg get me is the same Sc-c (the vector Ci-1,Ci,Ci+1 
> is considered as molecule vector)? where i used the united atoms force 
> field for my system.
> 

I'm still not clear what your problem is.  If you're not sure what the 
calculation is doing, then there are numerous literature references about lipid 
analysis that discuss the theory and application of deuterium order calculations.

-Justin

> thanks very much,
> Afsaneh
> 
> On Sun, Feb 7, 2010 at 7:14 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     afsaneh maleki wrote:
> 
>         Hi all,
> 
>         i used united the atom force field model for the membrane lipids
>         . to calculate order parameter i used :
>         g_order  -od   -d
>           i know united atom force field doesn't  have hydrogen atoms in
>         hydrocarbons chains .
>          i want to know gromacs calculates order parameter * Sc-c* or
>         *Sc-d* (Deuterium) ?
> 
> 
>     Simple geometry.
> 
> 
> 
>          in the output is written:  title "Deuterium order parameters"
> 
> 
>     Is that it?  If you've got an empty output, then your index file
>     probably wasn't prepared correctly.  There is a how-to on the
>     g_order page on the Gromacs website:
> 
>     http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order
> 
>     -Justin
> 
>         thanks in advance,
>         Afsaneh
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================