[gmx-users] order parameter in the unsaturated lipid

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 1 16:53:37 CET 2010

afsaneh maleki wrote:
> Hi,
> I am working on protein membrane that the lipid  have one the 
> _unsaturated _bond on C9-C10.The force Field  used is _united atom_.
> I have some questions.
> 1- Is Sc-c (order parameter)  valid for this lipid that contains  the 
> unsaturated bond?

Please see the -unsat option of g_order, and the accompanying warning about its use.

> 2- How to i calculate Sc-c  ?

Use g_order.

> 3- When i use g_order  -order , i obtain order.xvg file that contains 4 
> columns . What are the last third columns?

Check the header of the .xvg file; data sets are usually labeled quite clearly.


> thanks in advance very much, 
> Afsaneh Maleki


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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