From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Jun 30 2004 - 17:16:39 CDT
I have a hacked version of NAMD that prints out energies for all
interactions, but even looking at just the hundreds of torsions at each
timestep would be tedious. Have you done a whatif check on the last MD
structure just as a quick check?
Perhaps a small script to run the trajectory through VMD to pull out the
torsions would be feasible?
Brian
On Wed, 30 Jun 2004, Nicholas M Glykos
wrote:
>
> 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,
> Nicholas
>
>
> --
>
>
> Dr Nicholas M. Glykos, Department of Molecular
> Biology and Genetics, Democritus University of Thrace,
> Dimitras 19, 68100 Alexandroupolis, GREECE, Tel ++302551084037
> Fax ++302551084037, http://origin.imbb.forth.gr/~glykos/
>
*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
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