Comparing simulations using Amber 5 and Amber 6

From: Rebecca Perlow <>
Date: Thu 30 May 2002 10:18:36 -0400

Dear Amber users,
I am running MD simulations of a protein bound to 6 different
substrates. For each system, I have used the exact same parameters, the
parm99.dat parameter set. I have run 4 of the systems using Amber 5 and
now, due to the availability of resources, I was thinking of running the
remaining 2 systems using Amber 6. I would use the exact same protocol
with the Amber 6 systems as I did with Amber 5, but am wondering if the
results will be comparable. All of the systems would be run using the
same exact parameters, but 2 of the 6 run using Amber 6 rather than
Amber 5. Could I legitimately compare the trajectories of all 6 systems?
Thanks so much for your help.
-Rebecca Perlow

Rebecca Perlow, Ph.D.
Department of Biology
New York University
100 Washington Square East
New York, NY 10003
tel: (212)998-8228
Received on Thu May 30 2002 - 07:18:36 PDT
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