Dear Amber developers and users,
I am doing MD simulation on three structures. The initial structures are
from pdb files, which are 1KBH, 2C52 and 2KKJ.
I performed 1-step minimization, 7-step of heating and 50-ns equilibration
(5 ns each equilibration) by following the tutorial B3 using Amber 11 (2
nodes and 8 processors/node for equilibration).
And then, I independently repeated the exact simulation procedure.
Two structures with the lowest energy of 2C52 from the first run and
second run are identical. I also obtained the identical structures with
the lowest energy for 2KKJ. In contrast, two runs of 1KBH give me two
different structures.
My question, should we expect the identical results for two independent
simulation with the same procedure?
Any comments and suggestions will help.
Thanks,
Wu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 06 2011 - 18:00:02 PDT
