On Tue, Mar 27, 2007, Lachele Foley (Lists) wrote:
> 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?
Both trajectories use the mixed potential (1-lambda)*V0 + lambda*V1, so
the have indentical trajectories. V0 and its forces are computed on node 0,
and V1 and its forces are computed on node 1. But after the mixing is done,
both nodes have the same potential energy and forces. There can be problems
at the end points (just as in earlier versions of Amber). You might want to
talk with Thomas Steinbrecher about what he is putting in Amber 10: we're
looking for testers here anyway, and the new stuff should make it much easier
to create or annhiliate atoms.
>
> 2] The motions of the atoms in the system must depend on their
> masses.
The *dynamics* depends upon mass, but *thermodynamics* does not (in the
classical limit). That is, for equilibrium properties, you will get the same
results independent of the mass. This is why the code can use the same same
masses on both nodes, even if they are different in the physical system.
Look at whatever book you usually rely upon to explain statistical
thermodynamics: McQuarrie's "Statistical Mechanics" is a good choice if you
don't have some other book you are already familiar with.
...hope this helps...dac
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Received on Wed Mar 28 2007 - 06:07:47 PDT
