[gmx-users] index file for g_order

Milan Melichercik melicher at cray.dbp.fmph.uniba.sk
Mon Feb 2 16:05:02 CET 2004

On Mon, Feb 02, 2004 at 08:43:32AM +1100, Dallas Warren wrote:
> >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.

I thought just the same way, but t it didn't works. It generated file
(order.xvg) which contains only a header :(
Or if somebody knows how the atom groups should be, I will be pleased.


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