Free energy calculation yields strange results

From: Jun Zhang (
Date: Sun May 09 2010 - 07:53:36 CDT

Hi Everyone!

I am perfoming alchemical free energy calculation using NAMD 2.7b2. The transformation of the species is from chirality R to S

A(R) --- A(S)

in TIP3P water molecules. The box is about 50A. The species has a COO and I have use some ions (Na+ and Cl-) to neutralize it. I think the free energy should be ZERO since water is achiral. However, my result is 2328.95
kcal/mol, which made me surprised. My alchemical parameters set is:

alch on
alchType FEP
alchFile R2S_wb.fep
alchCol B
alchOutFile R2S_forward.fepout
alchOutFreq 10

alchVdwLambdaEnd 1.0
alchElecLambdaStart 0.5
alchVdWShiftCoeff 6.0
alchDecouple yes

alchEquilSteps 500
set numSteps 5000

set Lambda0 0.0
set dLambda 0.05

while {$Lambda0 <= 1.0} {

alchLambda $Lambda0
set Lambda0 [expr \$Lambda0 + \$dLambda]
alchLambda2 $Lambda0
minimize 500
run $numSteps


Can anyone give some suggestions? Thank you in advance.

Jun Zhang
Nankai University


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