[gmx-users] index file for g_order

Dallas Warren dallas.warren at vcp.monash.edu.au
Sun Feb 1 22:56:01 CET 2004

>I have a system which consist of lilid membrane, protein and water and I
>want to compute order paramaters for lilid molecules. The problem I have is
>I don't know how to create the proper index file for g_order by make_ndx.

Never used it myself, but my interpretation of the text that goes with the 
g_order program is that you need a group that contains each atom type you 
want to calculate the order parameter for.  For example with a C12 chain 
and you are interested in the order of the 6th carbon atom in the chain, 
then you need to generate a index file with a group that contains all of 
those 6th carbon atoms.  Using make_ndx, you will do that by separating out 
a particular atom type.  There is a line in the help when running make_ndx 
that tells you how to do that, type "h" after starting it.

"a C* & |a C CA will select all atoms starting with "C" but not the atoms 
"C" and "CA" ".

So something like  "a C6" will work if the 6th atom in the chain is 
numbered as C6.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
When the only tool you own is a hammer, every problem begins to resemble a nail.

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