negative free energies in 2D histogram

[Thomas Evangelidis]

Greetings,

I have run BEMD with 7CVs, but CV7 did not converge so I excluded the respective COLVAR, HILLS files and trajectory from my analysis with METAGUI. I did WHAM and then integrated (using "do_int2d.sh" script from the tutorial) the free energy of the 6 dimensional hypercubes to 2 dimensions in order to plot the free energy histogram. The procedure was the following:

for every X,Y pair of values:

calculate the sum of exp(-F/KT) (probability) of every 6D hypercube with X and Y coordinates, and at the end print
the X value, the Y value, and the -KT*log(sum) (free energy)

The problem is that there are some bins of the 2D histogram that have negative free energy, meaning probability > 1, which doesn't make sense. What am I doing wrong here? Just for a proof of concept, the same procedure worked fine for another similar case of mine where all 7 CVs did converge and thus were included in the analysis.

thanks,
Thomas

[Pratyush Tiwary]

Unless this is some WHAM peculiarity, free energies are only true up to a constant, so I would not worry about it. Just scale by subtracting out the minimum value from each data point.

- Pratyush

--

Pratyush Tiwary

Post-doctoral Researcher, ETH Zurich and USI Lugano

Department of Chemistry and Applied Biosciences

sites.google.com/site/pratyushtiwary/

--
You received this message because you are subscribed to the Google Groups "PLUMED users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to plumed-users...@googlegroups.com.
To post to this group, send email to plumed...@googlegroups.com.
Visit this group at http://groups.google.com/group/plumed-users.
To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/13c5e780-0129-4fe2-9090-d56bcafb7470%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.