**From:** Sharmon (*monsharmail_at_gmail.com*)

**Date:** Thu Jul 10 2014 - 13:29:29 CDT

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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

**Next message:**Kenno Vanommeslaeghe: "Re: two O atoms in CTER are unusually close"**Previous message:**Aron Broom: "Re: variable force constant"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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