DNA won't translocate through graphene nanopore

From: Priyanka Mondal (pmondal_at_udel.edu)
Date: Tue Aug 20 2019 - 14:04:52 CDT

Hi all,
I am trying to translocate dna through graphene nanopore. I followed steps
mentioned in tutorial in namd website and made sure that I applied electric
field is in -z direction. The pore size radius is 8A and I applied a field
of 0.2 V. I started with one DNA base already inside pore. After few ns
run, I see the dna retracting itself away from pore instead of
translocating through it. I am not sure what is causing it and how to fix
it. It will be nice if someone can help. Here is the namd script I am using
for applied bias :

#applied_bias.namd :
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
set sys agnr_dna_sol
set this ${sys}_EField
##set last ${sys}_min_cons
set last ${sys}_eq
#
###
numsteps 15000000 #600000
structure ../../../agnr_dna_sol_ions.psf
coordinates ../../../agnr_dna_sol_ions.pdb
###
outputName $this
XSTfile EField.xst
#
binCoordinates ../Constant_P/$last.restart.coor
binVelocities ../Constant_P/$last.restart.vel
###temperature 295
extendedSystem ../Constant_P/$last.restart.xsc
###
#### temperature control
langevin on
set TEMPP 295
langevinTemp $TEMPP
langevinFile ../../../langevin.pdb
langevinCol B

## pressure control
#useGroupPressure on
#useFlexibleCell yes
#useConstantArea yes
#langevinPiston on
#langevinPistonTarget 1.01325 # 1 atm
#
#langevinPistonTemp $TEMPP
#langevinPistonDecay 1000
#langevinPistonPeriod 2000
#
# parameters
parameters
 ../../../../../../../Packages/Force_Fields_CHARMM/toppar/par_all36_prot.prm
parameters
 ../../../../../../../Packages/Force_Fields_CHARMM/toppar/toppar_water_ions.mod.str
parameters
 ../../../../../../../Packages/Force_Fields_CHARMM/toppar/par_all36_na.prm

paraTypeCharmm on
exclude scaled1-4
1-4scaling 1

switching on
switchDist 10
cutoff 12
pairListDist 14
## integraion
timestep 2
rigidBonds all
nonBondedFreq 1
fullElectFrequency 4
stepsPerCycle 20

# output
binaryOutput yes
binaryRestart yes
wrapAll yes
wrapNearest yes
comMotion no
#
outputEnergies 1000
outputPressure 1000
outputTiming 1000
xstFreq 1000
dcdFreq 1000
restartFreq 1000

## electrostatics
pme on
pmeGridSizeX 90
pmeGridSizeY 95
pmeGridSizeZ 101

# external forces
constraints on
consKCol B
consRef ../../../harmonic_restrain.pdb
consKFile ../../../harmonic_restrain.pdb

## electric field
eFieldOn on
eField 0.0 0.0 0.0460

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Thank you in advance.

Priyanka Mondal,
Department of Physics and Astronomy,
University of Delaware,
USA

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