Then, please, let us know how it works for your systems. The results for my systems were exactly as expected. This allows to evaluate the order of the C-chains regardless their orientation... but I do not know if there is a better method to do this. I would be happy to know the opinion of anyone else who want to try this or to propose an alternative method.
Cheers, Ángel. On Wed, 2011-03-16 at 09:42 +0100, sa wrote: > Thank you Angel, I will try your suggestion. > > Cheers > > SA > > > > > Hi > very recently I faced the same problem with a system that > gives micelles > of different geometries and, as far as I saw, g_order don't do > that. > Then I decided to compute a kind of local order parameters > defined as: > > S_i=(3 cos(\theta)-1)/2 > > where theta is the angle between the segments joining the > carbon atoms > (i-1,i+1) and (i, i+2) in a linear C-chain. Perhaps you find > this > reasonable for your analysis... > > Cheers, > > Ángel. > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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