From: Canal de Sebassen (thecromicusproductions_at_gmail.com)
Date: Tue Aug 20 2019 - 23:37:50 CDT
I agree with Mohsen. In that PRL article they use 1V with a radius of
3.5nm. You're using 0.2V with a radius of 0.8nm, what (I'm not an expert on
this but I think) would lead to kind of a similar effect
On Tue, Aug 20, 2019 at 9:56 PM Mohsen Farshad <mohsen.farshad_at_maine.edu>
wrote:
> Hi,
>
> I think it is too narrow, I would increase it to 2-2.5 nm.
>
> Best,
> Mohsen
>
> On Aug 20, 2019 3:10 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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