AMBER Archive (2002)

Subject: Comparing simulations using Amber 5 and Amber 6

From: Rebecca Perlow (perlow_at_alum.mit.edu)
Date: Thu May 30 2002 - 09:18:36 CDT

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
e-mail: perlow_at_alum.mit.edu