AMBER Archive (2003)

Subject: AMBER: references about AMBER MD simulations

From: sd233_at_georgetown.edu
Date: Thu Aug 07 2003 - 00:23:35 CDT

Dear AMBER USERS:

When I looked at the RMS plot (using carnal), after running 500PS of
MD simulations with WATERBOX (size 16A) for a protein, the RMSD lies
around 0.4Angstroms from the initial structure. Is it a healthy
simulation?

Also Could anybody point out the references about AMBER MD simulations
for proteins with WaterBOX.

Thanks
Sincerely,
Sivanesan

D.Sivanesan, Ph.D.
Dept. of Oncology,
Lombardi Cancer Center,
Georgetown University, DC 20057

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