From: Jason Swails <>
Date: Wed, 28 Jan 2015 15:04:21 -0500

On Wed, Jan 28, 2015 at 2:44 PM, <> wrote:

> Pmemd14 does TI in the same way as sander does.

​Define "same way" :). There are important differences between how the
codes work (which is why the setups for both programs are so radically
different). The way I see it, pmemd DOES use a dual-topology approach...
you just have to crush those two topologies together and eliminate
duplicate terms beforehand.​

Simplified a bit, sander computes a lambda-weighted average of the two
topology files by computing both endpoints in their entirety and averaging
everything. By contrast, pmemd computes the same lambda-weighted average
by averaging the parts that are *different* and adding it to the parts that
are not. While the implementation (and by extension, using that
implementation) is drastically different, the two approaches are
mathematically identical.

> Both codes provide MBAR data. So one can easily compare how old a hat
> TI really is :-)
> ​

Yea -- MBAR here is used to optimize the use of TI data. I don't see how
MBAR is a viable alternative to any TI protocol that can't be done as a
simple single-step annihilation with no intermediate lambda values.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Jan 28 2015 - 12:30:03 PST
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