[gmx-users] index file for g_order
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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