question about FEP soft-core

From: yun luo (luoyun724_at_gmail.com)
Date: Mon Sep 14 2009 - 15:03:16 CDT

Hi,

I have a few question about the soft-core in NAMD. Does it include three
parameters as below or just fepVdwShiftCoeff ?
fepVdwShiftCoeff (delta in eq.28);
fepElecLambdaStart (related to Lambda(elec) in eq.28);
fepVdwLambdaEnd (related to Lambda(LJ) in eq.28)

The Vdw part in eq.28 use 6-3 LJ potential instead of typical 12-6 LJ
potential. Is it because the soft-core only apply to short-range Vdw
interactions (repulsive part of LJ potential)?
What's the major difference between NAMD soft-core and the WCA repulsive
pair potential used in CHARMM?

If I don't want use soft-core, should I set the three parameters as below?
epVdwShiftCoeff 0 (default value 5)
fepElecLambdaStart 0 (default value 0.5)
fepVdwLambdaEnd 1.0 (default value 1.0)

Thanks a lot!

Lyna

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