[gmx-users] g_order problems

[paloureiro at biof.ufrj.br]

> As I understand for the explanation I only have to construct a index file
> containing "only" the groups containing in each, one of the carbons from
> which I want to get the order parameter.  Just as an example let's say a
> group that contains all my C33 carbons. Well I have done that but as well as
> in other posts I been looking the resulting outputs files are empty. For my
> surprise when I add more groups of carbons to analyze some outputs numbers
> are appearing, and I always get a number of values equal as number of groups
> - 2. What does it mean?? the connectivity is taken from the tpr file or it's
> using the order of the groups of the index file?? Sorry I'm quite confuse any
> help will be appreciated.
>  

Hi Hector,

if your chain goes from C1 to C15, for instance, then you must create an index 
file containing (only!) the following groups:

[ C1 ]
...
[ C2 ]
...
...
[ C15 ]
...

If there are 15 carbons, there will be 13 order parameters.

Regards.

Pedro.