AMBER Archive (2007)Subject: AMBER: Amber 9 TI Details
From: Lachele Foley (Lists) (lf.list_at_gmail.com)
Date: Tue Mar 27 2007  15:03:20 CST
I want to make sure I fully understand the TI implementation in Amber
9 using multisander. I have two questions.
1] The manual says the two runs employ identical trajectories. How
are the equations of motion computed? Are the twin runs essentially
identical except that at each step hypothetical potentials are
calculated at lambda=0 and at lambda=1 for the dv/dl's? If not, then
are there any issues with, for example, cavity formation when
disappearing atoms?
2] The motions of the atoms in the system must depend on their
masses. If the masses do not change between the initial and final
states, then what sort of effect is expected in terms of
configurational sampling? If the changing atoms are restrained, I see
little reason to worry. But is it still ok if they are allowed to
move? The manual implies a statistical effect that minimizes the
issue: "in classical statistical mechanics, the Boltzmann distribution
in coordinates is independent of the masses, so this should not
represent any real restriction." Do you know a good reference for
that (with lots of gory details)?
Thanks!

:) Lachele
Lachele Foley
CCRC/UGA

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