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. Best, ~~~~~~~~~~~~ Michael Shirts Assistant Professor Department of Chemical Engineering University of Virginia michael.shi...@virginia.edu (434)-243-1821 On Mon, Oct 28, 2013 at 11:13 PM, Andrew S. Paluch <paluc...@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 > paluc...@miamioh.edu > (513) 529-0784 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
