[gmx-users] order parameter for UAFF model

[Justin A. Lemkul]

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
> 

-- 
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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

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