A development branch of the VMD plugin to analyze NAMD's free energy calculations
jhenin / parsefep Goto Github PK
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A development branch of the VMD plugin to analyze NAMD's free energy calculations
Which means removing the dependency on exectool for calling xmgrace. Should not be too complicated.
Hi @jhenin,
I don't know if this is the proper place to ask the question, but it seems that you are maintaining ParseFEP. I want to know how could parseFEP calculate error of the BAR estimator. I am aware of the original ParseFEP paper (J. Chem. Theory Comput. 2012, 8, 8, 2606โ2616). If eq. 14 is used to calculate the error, then the correlation lengths are necessary. For such calculation, J. Chem. Phys. 1989, 91, 461 was cited. However, the authors of the JCP paper claimed "In contrast, application of the blocking method to the correlation length requires ... This procedure is clearly not possible ...".
Thanks,
Haohao
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