how to set the input file for the free energy calculations with CHARMM Drude force field

From: Qasim Pars (qasimpars_at_gmail.com)
Date: Fri May 15 2020 - 17:36:33 CDT

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Dear users,

I would run the solvation free calculations of a ligand using NAMD-2.12
with CHARMM Drude force field but I don't know how to set up the input
file. Here are my questions:

What should I add to the below input file to run the simulations with
CHARMM Drude force field?

Should I use a minimization step for the solvation free energy
calculations? If yes, how?

The equilibrium and production steps would be 1 ns and 10 ns, respectively.
Are these settings are correct in the below input file?

# FORWARD DECOUPLE ON

# INPUT

set temp 300
temperature $temp
paraTypeCharmm on
exclude scaled1-4
1-4scaling 1.0

# TOPOLOGY

structure ligand.fep.psf

# INITIAL CONDITIONS

coordinates ligand.fep

# OUTPUT FREQUENCIES

outputenergies 10000
outputtiming 10000
outputpressure 10000
restartfreq 10000
XSTFreq 10000
DCDFreq 10000

# OUTPUT AND RESTART

outputname forward-on
restartname forward-on
binaryoutput no
binaryrestart no

# CONSTANT-T
langevin on
langevinTemp $temp
langevinDamping 2.0

# PME

PMEGridSpacing 1.0

# Periodic Boundary Conditions
cellBasisVector1 90. 0. 0.
cellBasisVector2 0. 90. 0.
cellBasisVector3 0. 0. 90.
cellOrigin 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 2.0
fullelectfrequency 2
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 500000
set numSteps 5500000

runFEPmin 0.0 0.0 0.0 $numSteps 10000 $temp
runFEP 0.0 1.0 0.05 $numSteps

Appreciate any help in advance!

Cheers,

-- 
Qasim Pars

• Next message: GILLET Natacha: "Issue in reading the soluteScalingFile for REST2"
• Previous message: M. A: "Fwd: FATAL ERROR: Charge placement error in QM-MM bond."
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