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Output

The output largely resembles that for wham, except with more columns. The first line echoes the command line, followed by a specification of the periodicity, and the number of windows. The iteration lines have the same meaning. When the current value for the PMF is dumped, the format looks like

-172.500000     -172.500000     1.968750        15.394489
-172.500000     -157.500000     2.574512        5.522757
-172.500000     -142.500000     3.147538        2.094142
-172.500000     -127.500000     3.505869        1.141952
where the first two columns are the values of the first and second dimensions of the reaction coordinate, the third column is the PMF, and the last column is the unnormalized probability.

Once the calculation has converged, wham will produce output resembling

# Dumping simulation biases, in the metadata file order 
# Window  F (free energy units)
#0       -0.000004
#1       -0.156869
#2       -0.534845
#3       -2.445469

These are the final F values from the wham calculation, and can be used for computing weighted averages for properties other than the free energy.

If you specified a nonzero number of Monte Carlo bootstrap error analysis trials, you will see lines that resemble

#MC trial 0: 990 iterations
#MC trial 1: 973 iterations
#MC trial 2: 970 iterations
#MC trial 3: 981 iterations
#MC trial 4: 984 iterations
at the end of the file.

The free energy data file is written when the calculation converges, and resembles:

-232.500000     -232.500000     4.812986        0.003185        0.000001        0.000000
-232.500000     -217.500000     4.830312        0.003741        0.000001        0.000000
-232.500000     -202.500000     4.898622        0.001009        0.000000        0.000000

The first two columns are the locations along the first and second dimensions of the reaction coordinate. The third is the free energy, while the fourth is the statistical uncertainty in the free energy. The fifth and sixth columns are the normalized probability and its statistical uncertainty. The two uncertainty columns will be zero if you did not use Monte Carlo bootstrapping.


next up previous contents
Next: Discussion Up: wham-2d Previous: File formats   Contents
Alan Grossfield 2007-11-13