AMBER Archive (2007)

Subject: AMBER: Can a simulation run on AMBER 9 be compared with another from AMBER 8?

From: ming hui (yongminghui_at_gmail.com)
Date: Tue Nov 06 2007 - 02:30:17 CST

Dear Amber users,

I have been using AMBER 8 to run standard MD simulations a protein and its
mutants for my project, however now due to restraints of my current computer
cluster, I have to use another cluster that only has AMBER 9 to simulate
some of the mutants.
If I use the same forcefield (or parameterize everything first in amber 8)
and my input parameters (ntf,ntt etc) are the same as those taken in AMBER
9, is there any significant difference in the way AMBER 9 works that would
make it unfair for me to compare the simulations that were run on different
versions? I know the thermodynamic integration method has changed, but I'm
not as sure about normal simulations.

Thank you

Regards,
Ming Hui

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