Subject: Re: CCL:CCL

From: Anton Feenstra <feenstra.-at-.chem.vu.nl>
Date: Wed, 07 Jan 2004 12:03:49 +0100

Rick Venable wrote:
> For a solvated protein simulation, I'd monitor the potential energy, the
> radius of gyration, and the bacbone RMSD relative to the starting
> structure.  When all 3 of these become flat, one could argue that
> the system is equilibrated; this could require 100s of picoseconds.

Although indeed one can argue this, it is hard to tell what 'flat' means
in a practical sense. For a seond-year lecture I give I have three slides
each giving the rmsd of a protein w/r to the x-ray structure. All three
of them level off to a nice plateau at the end, and appear to be genuinly
equilibrated in the way you define that. But, the three plots are of the
same simulation, the first of 0-100ps, the second of 0-1ns, and the last
of 0-10ns! If you overlay them, they are almost the same, except for the
scale of the axes! Those of you who'd like to see them, please ask me and
I can send you the three jpg files (~50k each).

While I don't regularly monitor r_gyr or e_pot, I don't know but suspect
that they would show similar behaviour... (although they may equilibrate
much faster than the rmsd).

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra.-at-.chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|