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From: Lachele Foley (Lists) <"Lachele>

Date: Tue, 27 Mar 2007 16:03:20 -0500

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!

Date: Tue, 27 Mar 2007 16:03:20 -0500

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 ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Wed Mar 28 2007 - 06:07:46 PDT

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