[gmx-users] Representative structure of a long simulation

[Y. U. Sasidhar]

But average structure may not really correspond to a physically sampled
structure.
Most populated conformation should be  the representative structure.
Sasidhar

Anton Feenstra wrote:

> "David L. Bostick" wrote:
> >
> > 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."
>
> May I then add to that the idea to optionally energy minimize the
> average structure, because in all likelyhood, some bond lengts,
> angles, etc. will probably be distorted in an average structure.
> A simple round of energy minimization will get you back to a
> 'realistic' structure.
>
> --
> Groetjes,
>
> Anton
>  ________ ___________________________________________________________
> |        | Anton Feenstra                                            |
> | .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
> | |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
> | |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
> | ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
> |  /  \  |-----------------------------------------------------------|
> | (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
> |  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
> |   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
> |  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
> | (    ) |-----------------------------------------------------------|
> |  \__/  | "We Have No Artefacts" (A. Visscher)                      |
> |________|___________________________________________________________|
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.