Re: Regarding: Free energy of alchemical transformation of K + and Na +

From: B.W.J. Irwin (
Date: Fri Jan 06 2017 - 08:50:24 CST

The sign of the change is defined by the direction of the
transformation. It should hold that

(K+ -> Na+) = -(Na+ -> K+)

are you doing the transformation in the same order? This could explain
the sign discrepancy?

Otherwise there could be many reasons?

- A Brief Check List -
Are you comparing against simulation results or experiment?
If simulation, is it the same force field and simulation parameters?
If experiment, is it justified that the simulation will reproduce the
experimental result?
Is the simulation 'converged' with respect to lambda windows etc.? Is
the density correct?
Is the water box large enough? bare ions can have long distance

Sorry if all this is very basic.


On 2017-01-06 11:09, Amit Kumar wrote:
> Hello NMAD Community,
> I'm alchemically transforming K+ into Na+ in a water box using CHARMM36
> force field. I got the free energy -23.40 Kcal/mol involved in this
> transformation while in some of literatures they have shown 16.70
> kcal/mol. What can be the reason of this difference ?
> I appreciate your suggestions.
> Best,
> Amit

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