[gmx-users] g_order problems

hseara at netscape.net hseara at netscape.net
Wed Nov 16 20:02:09 CET 2005

 Hello All,

I did simulation for 196*2 DOPS bilayer system. Using g_order I would like get order parameter for all the saturated carbons and also for the unsaturated ones. I'm quite confused on how to do it with the explanations in the manual and I wasn't able to find any useful post in the list.
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.
Thanks Hector
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