high temperature MD

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From: Anton Guliaev <anton_at_sgi1.lbl.gov>
Date: Fri 20 Aug 1999 16:51:28 -0700 (PDT)

Dear Amber Users,

I am trying to perform short high temperature MD (10-20ps) (Simulating
Annealing to some extent) only with restraints on hydrogen bonds and only
counter ions (no explicit solvent or NMR restraints). So far structures
(DNA) do not look very promising. However, using GROUP restraints (1.0) on
some residues (terminal for example) helps a lot and I can still see some
large conformational changes due to the temperature. Is it worth analyzing
this structures or GROUP restraints is too tight (even using 1.0) to
consider these structures for the conformational search.

I would really appreciate any feedback or relevant references

Anton
        *******************************************
        * Anton B. Guliaev, Ph.D *
      _ * Life Science Division * _
     / )* LBNL, Berkeley CA 94720 *( \
    / / * abguliaev_at_lbl.gov * \ \
  _( (_ * Tel: 510-486-5773 Fax: (510)-486-6488 * ) )_
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Received on Fri Aug 20 1999 - 16:51:28 PDT