Rst-wham: Difference between revisions
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Every 100 iterations, the current version of the PMF is dumped into the output file. These lines look like | 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 | -178.000000 0.014212 4909.138943 | ||
-174.000000 0.062631 4525.390035 | -174.000000 0.062631 4525.390035 | ||
-170.000000 0.227076 3432.434076 | -170.000000 0.227076 3432.434076 | ||
-166.000000 0.494262 2190.487110 | -166.000000 0.494262 2190.487110 | ||
-162.000000 0.817734 1271.708620 | -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. | 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 | Once the calculation has converged, wham will produce output resembling | ||
# Dumping simulation biases, in the metadata file order | # Dumping simulation biases, in the metadata file order | ||
# Window F (free energy units) | # Window F (free energy units) | ||
# 0 0.000004 | # 0 0.000004 | ||
# 1 -4.166136 | # 1 -4.166136 | ||
# 2 -3.241052 | # 2 -3.241052 | ||
# 3 -4.475215 | # 3 -4.475215 | ||
# 4 -6.324340 | # 4 -6.324340 | ||
# 5 -7.128731 | # 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. | 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. | ||
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If you specified a nonzero number of Monte Carlo bootstrap error analysis trials, you will see lines that resemble | 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 0: 990 iterations | ||
#MC trial 1: 973 iterations | #MC trial 1: 973 iterations | ||
#MC trial 2: 970 iterations | #MC trial 2: 970 iterations | ||
#MC trial 3: 981 iterations | #MC trial 3: 981 iterations | ||
#MC trial 4: 984 iterations | #MC trial 4: 984 iterations | ||
at the end of the file. | at the end of the file. | ||
The free energy data file is written when the calculation converges, and resembles: | The free energy data file is written when the calculation converges, and resembles: | ||
#Coor Free +/- Prob +/- | #Coor Free +/- Prob +/- | ||
-178.000000 0.014386 0.000098 0.106389 0.000017 | -178.000000 0.014386 0.000098 0.106389 0.000017 | ||
-174.000000 0.068560 0.000151 0.097128 0.000025 | -174.000000 0.068560 0.000151 0.097128 0.000025 | ||
-170.000000 0.250825 0.000350 0.071496 0.000042 | -170.000000 0.250825 0.000350 0.071496 0.000042 | ||
-166.000000 0.523786 0.000294 0.045186 0.000022 | -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. | 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> | ||
|} | |} | ||