Re: DIHEDral drift [2] ?

From: Nicholas M Glykos (
Date: Wed Jun 30 2004 - 13:08:14 CDT

Hi Brian,

> I can't remember if you send that you checked for "bad" initial dihedral
> energies. It might be one really bad interaction that is slowly working
> it self out within the terms of the force field.
> Did you do a "whatif" check on the initial structure?

The structure is fully validated [and because the structure was determined
in this part of the world I know firsthand that the maps (at 2.3A resolution)
were beautiful].

The thing that makes me feel that it may be a problem with our simulation
parameters, is that I have observed the same drift on two completely
independent simulations, one of a small 4-alpha-helical bundle (110 amino
acids, 22000 atoms total, NAMD 2.5b1), and this one (320 amino acids,
~54000 atoms, NAMD 2.5 latest). The trouble is that I'm not sure where
to start from. Would it be possible (through an analysis of the trajectory)
to identify the slow varying contribution to the dihedral energy term ?

Thanks again,

            Dr Nicholas M. Glykos, Department of Molecular
        Biology and Genetics, Democritus University of Thrace,
    Dimitras 19, 68100 Alexandroupolis, GREECE, Tel ++302551084037
      Fax ++302551084037,

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