[gmx-users] order parameter for UAFF model

Justin A. Lemkul jalemkul at vt.edu
Sun Feb 7 16:44:41 CET 2010

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:



> thanks in advance,
> Afsaneh


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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