Re: [AMBER-Developers] hydrogen mass repartitioning

From: Adrian Roitberg <>
Date: Wed, 12 Mar 2014 17:49:35 -0400


I am glad Dave caught that !

indeed, the final 'a.' is my way of signing off, not the chosen option ;-)

As for 'it works' I clearly mean thermodynamics. That I can actually
justify analytically. The kinetics just happens to be correct also. We
did alanine_10 and counted transitions between basins and we get the
same results with 2fs or 4fs within error bars. It is of course harder
to formalize that result. Large conformational changes are probably 'ok'
in time scale (as 'ok' as with 2 fs..) since the changes with HMR
conserve local mass and moments of inertia within each residue.


On 3/12/14 3:17 PM, David A Case wrote:
> On Wed, Mar 12, 2014, Adrian Roitberg wrote:
>> I agree with Scott
>> When we started looking into this, my idea was that either
>> a. it breaks, so we say bad things about other programs
>> or
>> b. it works, so we gain a factor of 2 in speed..
>> a.
> So, is the final "a." your initial, or your choice between the two
> alternatives listed above?
> Further, the "it works" might be true in a thermodynamic sense (==correctly
> samples the Botzmann distrbution), or might also be true in a kinetic sense
> (==rates of hopping among basins is roughly unchanged as well).
> ...dac
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> AMBER-Developers mailing list

                             Dr. Adrian E. Roitberg
Colonel Allan R. and Margaret G. Crow Term Professor.
Quantum Theory Project, Department of Chemistry
University of Florida
AMBER-Developers mailing list
Received on Wed Mar 12 2014 - 15:00:03 PDT
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