[gmx-users] Representative structure of a long simulation

David L. Bostick dbostick at physics.unc.edu
Thu Apr 25 15:27:11 CEST 2002

This may seem too simple for you, but if I were looking for a
"representative" structure of a protein, I would just take the time
averaged structure.  You can do this easily by making an index group for
your protein atoms, and do g_covar on the last say 5 ns of your
simulation.. just to be sure you are getting data corresponding to
equilibrium.  If you are really unsure, you can just use the last 1 or 2
ns.  if you use the option -av , the program will spit out the average
structure over the trajectory.  This should be "representative."


David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165 
Program in Molecular and Cellular Biophysics 
UNC-Chapel Hill					
CB #3255 Phillips Hall				dbostick at physics.unc.edu	
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick	

On Thu, 25 Apr 2002, Marc Baaden wrote:

> Hi,
> the following might be a trivial/basic question, but I would like
> to get as many comments/different ideas/views as possible.
> I have a long (10 ns) simulation of a membrane protein system, and
> would like to use one protein structure out of this simulation as
> starting point for some further (simple) studies. So I am somehow
> looking for the most "representative" structure out of these 10 ns.
> My idea was to use the clustering approach, and go for the cluster
> which is predominant (in the sense of nb of occurrences), using its
> central structure.
> Nevertheless there is simply too much data (10 ns * high save frequency)
> too run a cluster analysis on the whole thing. So what is the right way
> in order not to "miss" anything ?
> Or would you suggest another approach ? (eg based on energies ? ..)
> thanks for your comments,
> Marc Baaden
> -- 
>  Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
>  mailto:baaden at smplinux.de  - ICQ# 11466242 -  http://www.marc-baaden.de
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