Re: DNA won't translocate through graphene nanopore

From: Canal de Sebassen (thecromicusproductions_at_gmail.com)
Date: Tue Aug 20 2019 - 19:43:37 CDT

Is the DNA single or double stranded? If the pore is too small, you may
have a big entropic contribution that doesn't allow it to translocate.
You can also be in front of this phenomenon
https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.120.268101

On Tue, Aug 20, 2019 at 3:06 PM Priyanka Mondal <pmondal_at_udel.edu> wrote:

> 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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