[gmx-users] Representative structure of a long simulation

[Anton Feenstra]

"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)                      |
|________|___________________________________________________________|