[gmx-users] order parameters for unsat. carbons

David van der Spoel spoel at xray.bmc.uu.se
Sat Nov 26 12:35:10 CET 2005

Kia Balali-Mood wrote:

>Dear All,
>I was wondering if anyone can enlighten me on how order parameters are 
>calculated for unsaturated carbons (eg. carbons 9 and 10 on oleoyl chains)on 
>I understand how they are calculated for saturated carbons. I thought I 
>understood how they are done for unsaturated carbons but apparently not!
>The reason for my query is that a collaborator in London has a NAMD trajectory 
>of a related membrane bound protein (we, of course have a gmx trajectory!)
>On the Tcl script that the collaborator had generated we are getting 
>significantly different values to that generated from g_order. 
Check old papers by Marrink, Tieleman and Van Buuren. The definition 
given in the header of g_order is:

Compute the order parameter per atom for carbon tails. For atom i the vector
i-1, i+1 is used together with an axis. The index file has to contain a 
with all equivalent atoms in all tails for each atom the order parameter has
to be calculated for. The program can also give all diagonal elements of the
order tensor and even calculate the deuterium order parameter Scd (default).
If the option -szonly is given, only one order tensor component 
(specified by
the -d option) is given and the order parameter per slice is calculated as
well. If -szonly is not selected, all diagonal elements and the deuterium
order parameter is given.

>Sometime ago (in my PhD days over in Edinburgh Univ.) I enquired about the 
>possibility of setting up a gromacs users meeting!
>Some of you suggested having something in the summer....
>I'm prepared to help!
We are considering organizing a tuturial/user meeting sometime next year.

>kind regards

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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