### Regression test of NPT ensemble using flat files
### System: Water900
## Reading low temperature result
## Reading high temperature result
## Validating ensemble
Analytical slope of ln(P_2(V)/P_1(V)): -2.42930431
Trajectory 1 equilibration: First 104 frames (10.4% of trajectory) discarded for burn-in.
Trajectory 1 decorrelation: 127 frames (14.2% of equilibrated trajectory) discarded for decorrelation.
Trajectory 1 tails (cut = 0.10%): 2 frames (0.26% of equilibrated and decorrelated trajectory) were cut
After equilibration, decorrelation and tail pruning, 76.72% (768 frames) of original Trajectory 1 remain.
Trajectory 2 equilibration: First 0 frames (0.0% of trajectory) discarded for burn-in.
Trajectory 2 decorrelation: 0 frames (0.0% of equilibrated trajectory) discarded for decorrelation.
Trajectory 2 tails (cut = 0.10%): 2 frames (0.20% of equilibrated and decorrelated trajectory) were cut
After equilibration, decorrelation and tail pruning, 99.80% (999 frames) of original Trajectory 2 remain.
Overlap is 86.6% of trajectory 1 and 83.5% of trajectory 2.
A rule of thumb states that a good overlap is found when dP = (2*kB*T)/(sig),
where sig is the standard deviation of the volume distribution.
For the current trajectories, dP = 100.0, sig1 = 0.02 and sig2 = 0.01.
According to the rule of thumb, given P1, a good dP is dP = 324.6, and
                                given P2, a good dP is dP = 349.7.
Rule of thumb estimates that dP = 337.2 would be optimal (currently, dP = 100.0)
Computing log of partition functions using pymbar.BAR...
Using 65.88726 for log of partition functions as computed from BAR.
Uncertainty in quantity is 0.01435.
Assuming this is negligible compared to sampling error at individual points.
Computing linear fit parameters (for plotting / comparison)
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Linear Fit Analysis (analytical error)
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Free energy
    174.73873 +/- 9.85638
Estimated slope                  |  True slope
    -6.441826 +/- 0.363232       |  -2.429304
    (11.05 quantiles from true slope)
Estimated dP                     |  True estimated dP
    265.2  +/- 15.0              |  100.0 
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Computing the maximum likelihood parameters
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Maximum Likelihood Analysis (analytical error)
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Free energy
    183.34577 +/- 9.77923
Estimated slope                  |  True slope
    -6.750323 +/- 0.360414       |  -2.429304
    (11.99 quantiles from true slope)
Estimated dP                     |  True estimated dP
    277.9  +/- 14.8              |  100.0 
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Computing bootstrapped maximum likelihood parameters... [0/3]
Computing bootstrapped maximum likelihood parameters... [1/3]
Computing bootstrapped maximum likelihood parameters... [2/3]
Computing bootstrapped maximum likelihood parameters... [3/3]
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Maximum Likelihood Analysis (bootstrapped error)
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Free energy
    183.34577 +/- 11.66193
Estimated slope                  |  True slope
    -6.750323 +/- 0.429086       |  -2.429304
    (10.07 quantiles from true slope)
Estimated dP                     |  True estimated dP
    277.9  +/- 17.7              |  100.0 
==================================================
Calculated slope is 10.1 quantiles from the true slope
