From: Francesco Coppola (
Date: Wed Feb 08 2023 - 11:33:42 CST

Dear community,

I hope you can help me with my perplexity.
I'm trying to use the BFEE on an interaction between a protein (to which I
applied a constraint during equilibration) and a small peptide. During the
simulation I can see that they are stably interacting.

When I go to use the BFEE, however, I get a non-negative value that leaves
me perplexed. I am attaching here the details of the result.

[image: image.png]

Comparing with what I see on the BFEE explanation page, this is the value
that is not in line with my calculation:

(1/beta)*ln(S*I*C0) = +0.81 kcal/mol

Could you explain to me why? What does this step refer to? Because if I
compare with the vmd-explanation page, here I should expect at least a
two-digit negative value.

Thank you so much for your help and time
Best regards