[gmx-users] lmc-stats

Michael Shirts mrshirts at gmail.com
Tue Oct 29 06:23:11 CET 2013

Hi, Andrew-

The choice of lmc-stats only affects the calculation of the weights,
it does not affect the calculation of the transition matrix.

There are two possibilities for the transition matrix; the estimated
one (which is just called 'Transition Matrix' -- we should probably
have a better name), and the empirical one.  The empirical transition
matrix is just transition counts. The first one is an ensemble average
of P(k|x); for neighbor moves, this is just the average of the barker
transition probabilities (plus the choice of going up or down),

Let me know if this is useful.  Not that many people have used this
code, thus there are likely ways that it can be improved for better
utility.  I generally haven't tried to calculate free energy
differences from the transition matrix, though it should give
consistent results with the other methods.

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

On Mon, Oct 28, 2013 at 11:13 PM, Andrew S. Paluch <paluchas at miamioh.edu> wrote:
> When performing free energy calculations using the expanded ensemble method,
> there is a barker and metropolis option for lmc-stats. Are the corresponding
> transition probabilities computed with or without the weighting factors?
> That is, are these probabilities biased or not?
> Thank you,
> Andrew
> --
> Andrew S. Paluch, PhD
> Department of Chemical, Paper, and Biomedical Engineering
> Miami University
> PaluchAS at MiamiOH.edu
> (513) 529-0784
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