soft-core FEP in namd 2.7b

From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Fri May 08 2009 - 11:57:10 CDT

Dear All,

I have some trouble interpreting the new parameters (listed below) in
the namd 2.7b manual's FEP chapter.
Here are my interpretations, I would be glad if you could check them
with me:

I assume that decouple is set to "on".

manual p. 118:
"fepVdwShiftCoeff / tiVdwShiftCoeff":
considered are only vdW interactions between the growing/shrinking
particles and their respective environments only.
(otherwise: what's the use of soft-core for vdW of the environment with
itself?)

"fepElecLambdaStart/tiElecLambdaStart ":
considered are only the elect. interactions of the growing particles
with its environment:
E_el(0.5)=0 linearly increased to E_el(1.0)=full strength
(my thinking is that interactions between the shrinking particles with
the environment are *decreasing*)

p. 119:
"fepVdwLambdaEnd / tiVdwLambdaEnd":
it means that @lambda>0.5, we set fepVdwShiftCoeff (tiVdwShiftCoeff) to
zero.

Is this all correct?
If yes, then @lambda=0, I see an abrupt transition from "hard-core" to
"soft-core" for vdW interactions between shrinking particles and their
environment.
Is the corresponding free energy difference negligible with the default
fepVdwShiftCoeff value of 5A^2? If not, how can one practically measure
this free energy difference?

Thank you,
Best,
Sebastian

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