[gmx-developers] Re: Energy Minimization (was gmx-developers Digest, Vol 62, Issue 2)

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jun 4 12:37:03 CEST 2009

Hi Igor,

>>>>> 1) Since a dynamics of complex biological system depends on quality of
>>>>> the
>>>>> minimized structure, a fine minimization is very important.

The dynamics does not depend on the quality of the minimized structure
but on the probability that the starting configuration is part of the
ensemble you're investigating.

> There is no rigorous prove in the manual section 3.10 that the finer
> energy minimization is not essential for MD of complex biological system.

There doesn't need to be. That section describes the methods. By the
way, I haven't seen rigorous prove against the existence of
leprechauns or the monster of Loch Ness yet.

> This seems to be in contardiction with the statement that "steep"
> minimization produces good enough structure for MD.

This is true only if your starting structure is close enough to a
structure that has sufficient relevance for the ensemble you're trying
to sample. What you describe seems to point to severe problems with
your initial configuration that can't be resolved with energy
minimization. Double check the topology and the configuration to
eliminate these as the source of the problem.



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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