AMBER Archive (1999)

Subject: high temperature MD

From: Anton Guliaev (anton_at_sgi1.lbl.gov)
Date: Fri Aug 20 1999 - 18:51:28 CDT

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
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        * Anton B. Guliaev, Ph.D *
      _ * Life Science Division * _
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    / / * abguliaev_at_lbl.gov * \ \
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