Regarding free energy cost incurred by using pseudo bonds

From: Sharmon (
Date: Thu Jul 10 2014 - 13:29:29 CDT

Hello All,

I had restrained my system during free energy calculations (FEP during all
intervals) using flat bottom restraints (for some distances) via a tcl
script. Now, to subtract the cost associated with these restraints, I have
done further calculations where the forces are going to zero by scaling
down the force constants, such as multiplying force constants with factor
which goes from 1 to 0 in decrements of 0.1. I also write out the energies
associated whenever the restraints are applied. Note that the restraints
are not applied always.

Now, I have a question that whether I should be using the tcl energies for
calculating the cost incurred by restraints?If yes, how should the formula
will look like for free energy estimation.

Or We need to do it in the way as we do in FEP, take the energies from the
namd log file and treat the decrement as in lambda interval.

What should be the correct way? I know this might sound naive, but it is
confusing me from the practical application point of view.

Any help will be greatly appreciated!

Thanking you

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