[gmx-users] bootstrapping of PMF

Alex alexanderwien2k at gmail.com
Wed Nov 9 17:11:52 CET 2016

Dear gromacs user,

I have performed a US simulation to find PMF of a peptide adsorbed to a
solid surface.

I have already evaluated the result by bootstrapping in gmx WHAM using the
b-hist method and 600 number of bootstraps and 1200 bins also with
considering the integrated autocorrelation time into account

Here is the command:

gmx wham -hist Histo.xvg -nBootstrap 600 -bins 1200 -bs-method b-hist
-bsres bsResult.xvg -bsprof bsProfs.xvg -if Fpull.dat -it TPR.dat -min 1.95
-max 4.7 -ac -o Profile.xvg -zprof0 4.69

And here are the result:



iact.xvg   integrated autocorrelation time

My first question is that if I have well converged PMF result, based on
above files?

I was also wondering that what exactly I have to be reported later in for
example a publication and ... ? the normal profile.xvg with out bootstrap
or this bsProfs.xvg? What is the difference between bsProfs.xvg and the
normal profile.xvg that we can get from normal gmx WHAM with out

And why the first 130 lines of iact.xvg file have been autocratically
commented out from  the rest?

And finally, do we always and here need to correct all the PMF profile by
the "$k_{B}T*log[4π(\epsilon)^2]$" factor in which \epsilon is reaction
coordinate? as been mentioned here:
Hub, J. S.; de Groot, B. L.; van der Spoel, D.J. Chem. Theory
Comput.2010,6, 3713-3720

Many thanks for your comments in advance.


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