NAMD overestimates the hydration free energy with Drude force field

From: Qasim Pars (qasimpars_at_gmail.com)
Date: Tue Jul 14 2020 - 12:10:01 CDT

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Dear NAMD users,

I calculated the hydration free energy (HFE) of a molecule with CHARMM
Drude force field but NAMD overestimates (about -1.7 kcal/mol) the
hydration free energy of that molecule. Do you have any idea why the
NAMD-2.13 overestimates the HFE?
Is there anything wrong in my simulation parameters below? E.g. Is the
"runFEPmin" line correct for the forward and backward simulations?

#########################
###### FORWARD ON ######
#########################
set temp 300
temperature $temp

parameters toppar_drude_master_protein_2013f.str
paraTypeCharmm on

# DRUDE PARAMETERS
drude on
drudeTemp 1
drudeDamping 20.0
drudeNbtholeCut 5
drudeHardWall on
drudeBondLen 0.2
drudeBondConst 40000

exclude scaled1-4
1-4scaling 1.0

# TOPOLOGY
structure solvated_ligand.psf

# INITIAL CONDITIONS
coordinates solvated_ligand.pdb

# OUTPUT FREQUENCIES
outputenergies 10000
outputtiming 10000
outputpressure 10000
restartfreq 10000
XSTFreq 10000
DCDFreq 10000

# OUTPUT AND RESTART
outputname forward
restartname forward

binaryoutput no
binaryrestart no

# CONSTANT-T
langevin on
langevinTemp $temp
langevinDamping 2.0

# PME
PME yes
PMETolerance 10e-6
PMEInterpOrder 4
PMEGridSpacing 1.0

# Periodic Boundary Conditions
cellbasisvector1 30.0 0.0 0.0
cellbasisvector2 0.0 30.0 0.0
cellbasisvector3 0.0 0.0 30.0
cellOrigin 0.0 0.0 0.0

# WRAP WATER FOR OUTPUT
wrapWater on

# CONSTANT-P
LangevinPiston on
LangevinPistonTarget 1
LangevinPistonPeriod 100
LangevinPistonDecay 100
LangevinPistonTemp $temp

StrainRate 0.0 0.0 0.0
useGroupPressure yes

useFlexibleCell no

# SPACE PARTITIONING
stepspercycle 20

# CUT-OFFS
switching on
switchdist 10.0
cutoff 12.0
pairlistdist 14.0

# RESPA PROPAGATOR
timestep 1.0
fullelectfrequency 1
nonbondedfreq 1

# SHAKE
rigidbonds all

# COM
ComMotion no

# FEP PARAMETERS
source fep.tcl
alch on
alchType fep
alchFile ligand.fep
alchCol B
alchOutFile forward-on.fepout
alchOutFreq 100
alchVdwLambdaEnd 1.0
alchElecLambdaStart 0.5
alchVdWShiftCoeff 4.0
alchDecouple on

alchEquilSteps 100000
set numSteps 10000000

runFEPmin 0.0 0.0 0.0 $numSteps 1000 $temp
runFEP 0.0 1.0 0.05 $numSteps

###########################
###### BACKWARD ON ######
###########################
set temp 300
temperature $temp