DIHEDral drift ?

From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
Date: Thu Jun 10 2004 - 13:15:09 CDT

Dear All,

We are running a 6 ns NPT simulation of a ~60000 atom system (using the
latest stable NAMD version) and we observe a very slow equilibration of
the dihedral energy term (or is it a drift ?). To make things easier to
visualise, I've put-up a picture showing the evolution of various terms

         http://utopia.duth.gr/~glykos/MD_namd_list.png (88 KBytes)

For the run shown we use Nose-Hoover Langevin dynamics (320K, 1atm) with a
2 fs step, periodic boundary conditions, PME evaluation every four
timesteps, Shake, and (hopefully) suitable switching functions. The
structure of the protein has been and still is fairly stable.

Any insight as to why the dihedral energy term is taking so long to
equilibrate would be greatly appreciated,

Best regards,

           Dr Nicholas M. Glykos, Department of Molecular
        Biology and Genetics, Democritus University of Thrace,
    Dimitras 19, 68100 Alexandroupolis, GREECE, Tel ++302551084036
      Fax ++302551084037, http://origin.imbb.forth.gr/~glykos/

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