Rst-wham: Difference between revisions
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The time series files must follow one of two formats, depending on whether the temperature was specified in the metadata file. If no temperature was specified, the file should contain two columns, where the first is the time (which isn't actually used), and the second is the position of the system along the reaction coordinate. Both numbers should be in floating point format. Lines beginning with "#" are ignored as comments. Additional columns of data are ignored. | The time series files must follow one of two formats, depending on whether the temperature was specified in the metadata file. If no temperature was specified, the file should contain two columns, where the first is the time (which isn't actually used), and the second is the position of the system along the reaction coordinate. Both numbers should be in floating point format. Lines beginning with "#" are ignored as comments. Additional columns of data are ignored. | ||
If the simulation temperature is specified, there must be a third column of data, containing the system's potential energy at that time point. It should be a floating point value. | If the simulation temperature is specified, there must be a third column of data, containing the system's potential energy at that time point. It should be a floating point value. | ||
</span> | |||
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|<span style="color: blue;">freefile</span><br/><span style="margin-left: 0px;"> | |||
The first line of the output file contains echoes command line. The next line or two contain comments describing the periodicity used and the number of simulation windows present. While the calculation is running, it will print out lines that look like the following: | |||
<code>#Iteration 10: 0.106019 | |||
#Iteration 20: 0.062269 | |||
#Iteration 30: 0.039890 | |||
#Iteration 40: 0.027003</code> | |||
This specifies the current iteration number, and the average change in the F values for the current iteration. This number is not used for deciding when the calculation has converged; rather, the maximum change, as opposed to the average, is used. | |||
Every 100 iterations, the current version of the PMF is dumped into the output file. These lines look like | |||
-178.000000 0.014212 4909.138943 | |||
-174.000000 0.062631 4525.390035 | |||
-170.000000 0.227076 3432.434076 | |||
-166.000000 0.494262 2190.487110 | |||
-162.000000 0.817734 1271.708620 | |||
The first column is the value of the reaction coordinate, the second is the value of the PMF, and the third is the unnormalized probability distribution. | |||
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 -4.166136 | |||
# 2 -3.241052 | |||
# 3 -4.475215 | |||
# 4 -6.324340 | |||
# 5 -7.128731 | |||
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. | |||
You may have noticed that all of the lines except the free energies are preceded by "#". This allows you to check convergence of your wham calculation by simply plotting the output file in gnuplot. If the free energy curves have stopped changing, your tolerance is small enough. | |||
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: | |||
#Coor Free +/- Prob +/- | |||
-178.000000 0.014386 0.000098 0.106389 0.000017 | |||
-174.000000 0.068560 0.000151 0.097128 0.000025 | |||
-170.000000 0.250825 0.000350 0.071496 0.000042 | |||
-166.000000 0.523786 0.000294 0.045186 0.000022 | |||
The first column is the value of the reaction coordinate, the second is the free energy. The third is the statistical uncertainty of the free energy (which is only meaningful if you performed Monte Carlo bootstrapping). The fourth and fifth columns are the probability and it's associated statistical uncertainty. Again, the latter is only meaningful if bootstrapping is performed. See section for further discussion of error estimation. | |||
</span> | </span> | ||
|} | |} | ||