From: Kei-ichi Okazaki (keiichi.okazaki_at_nih.gov)
Date: Fri Jan 27 2012 - 18:16:47 CST
Dear NAMD users,
I am trying to calculate solvation free energy of a small molecule by
thermodynamic integration (TI).
And I have a question about output file of TI.
I set up configuration file for TI with soft-core potential as below.
I set "alchElecLambdaStart 0.5" and "alchVdwLambdaEnd 0.5" to separate
the scaling of vdW and electrostatics, that is, vdW is turned on first
for 0<=lambda<=0.5 and then, ele is turned on for 0.5<=lambda<=1.0.
And in the output, Elec_dU/dl and vdW_dU/dl are reported as below.
When I saw the output of lambda=0.1, for example, I was confused because
Elec_dU/dl takes some values even though ele is not turned on yet.
I suspect that it just reports Elec_dU/dl for lambda=0.0, but it cannot
be used for TI calculation because there should not be any contribution
from ele for lambda<0.5.
Is my guess right? I appreciate any suggestions.
Thanks in advance.
Kei-ichi Okazaki, PhD
## configuration file #########################################
# Free energy perturbation
alch On # Enable alchemical simulation module
alchType ti # Set method to thermodynamic integration
alchFile ../../Common/h2p.box20.alchem.pdb # PDB file with
perturbation flags
alchCol B # Perturbation flags in Beta column
alchOutfile $outputname.out
alchOutFreq 1000
alchEquilSteps 500000
alchVdWShiftCoeff 6.0 # Enable soft-core vdW potential
alchElecLambdaStart 0.5 # Introduce electrostatics for lambda > 0.0
alchVdwLambdaEnd 0.5
alchLambda 0.1
alchLambda2 0.1
## output file #################################################
# STEP Elec_dU/dl Elec_avg vdW_dU/dl
vdw_avg Elec_dU/dl Elec_avg vdW_dU/dl
vdw_avg PME_dU/dl PME_avg
# <---------------------PARTITION 1------------------------>
<---------------------PARTITION 2--------------------->
#NEW TI WINDOW: LAMBDA 0.1
#PARTITION 1 VDW LAMBDA 0.2
#PARTITION 1 ELEC LAMBDA 0
#PARTITION 2 VDW LAMBDA 1
#PARTITION 2 ELEC LAMBDA 0.8
TI 0 -452.9840 -452.9840 -9.6522
-9.6522 0.0000 0.0000 0.0000 0.0000
TI 1000 -228.3854 -228.6098 1.7409
1.7296 0.0000 0.0000 0.0000 0.0000
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