Tutorial-l Mailing List

From: Athreya, Nagendra Bala Murali (nathreya_at_illinois.edu)
Date: Mon Dec 05 2016 - 16:27:21 CST

Hi Jeff,

Thank you very much for your reply. I did go through the paper. I think I kept the gridForce just to make sure that DNA doesn't stick to Graphene.

The dielectric constant is HUGE when it is non-rigid. I did not know that. This is a great info!

I have made the changes and submitted the job for running the simulation. I will get back to you after it has run for few ns. (I am hoping that with these changes I should be able to see the translocation by the first few ns).

Also, though the model with Graphene and DNA is just around ~10,000 atoms, when I add the water and ions, it increases to ~ 400,000 atoms. Is there any way to reduce the number of water atoms?

Thank you once again for your help and time.

Sincerely,
Nagendra Athreya
________________________________________
From: Jeff Comer [jeffcomer_at_gmail.com]
Sent: Thursday, December 01, 2016 9:14 AM
To: Athreya, Nagendra Bala Murali
Cc: tutorial-l_at_ks.uiuc.edu
Subject: Re: tutorial-l: DNA not translocating - Nanopore tutorial

Hi,

First, if you're not already aware of it, you should have a look at this paper:

http://dx.doi.org/10.1021/nl301655d

What are you using the gridForce for? I don't see any reason to use it
with this system. Does the DNA translocate with the gridForce turned
off?

The DNA tends to adhere to the surface, which may be why you aren't
seeing translocation. It also likely depends on the size of the pore.
You might also want to check that lengthZ is being set correctly. Add
the following to the bottom of your file:

print "lengthZ $lengthZ"

Although we did not use rigidBonds in the tutorial (this should
probably be amended), as has been noted on this list previously, it's
an incorrect application of the CHARMM force field. CHARMM is
parameterized for rigid water and rigid bonds to hydrogen. Also, using
rigidBonds will make your simulation faster by allowing you to use a 2
fs timestep. Moreover, flexible TIP3P water has an unrealistically
large dielectric constant, which is important for simulations such as
yours involving highly charged species. I calculate a dielectric
constant of 165 for flexible TIP3P and 99 for rigid TIP3P.

I would recommend this:
# integration
rigidBonds all
timestep 2
nonBondedFreq 1
fullElectFrequency 2
stepsPerCycle 10

Your system is HUGE. Maybe you should try with a small system first
with a short piece of DNA until you get the protocol established. A
minimal system could probably have ~40,000 atoms. This might also help
you to pin down what is causing the lack of translocation without
having to run for weeks.

Regards,
Jeff

末末末末末末末末末末末末末末末末末沫覧覧覧
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
Website: http://jeffcomer.us

On Wed, Nov 30, 2016 at 8:46 PM, Athreya, Nagendra Bala Murali
<nathreya_at_illinois.edu> wrote:
> Hello,
>
> I am modeling a DNA nanopore system similar to the one mentioned in the nanopore tutorials. I am using Graphene instead of Silicon Nitride.
>
> I have a dsDNA of about 60 bp long. The system consists of ~1.5 million atoms (water + ions included).
>
> This is NAMD file I have:
>
> *******************************************************************************************
> set voltage 1.0
> set xsc scaled_${sys}_ions.xsc
>
> set this ${sys}_${voltage}V_1
> #set last ${sys}_eq
> set next ${sys}_${voltage}V_2
>
> numsteps 20000000
> structure ${sys}_ions.psf
> coordinates scaled_${sys}_ions.pdb
>
> outputName $next
> binCoordinates $this.restart.coor
> binVelocities $this.restart.vel
> extendedSystem $this.restart.xsc
> #extendedSystem $xsc
>
> # temperature control
> langevin on
> langevinTemp 295
> langevinFile ${sys}_langevin.pdb
> langevinCol B
>
> # parameters
> parameters ../c32b1/toppar/par_all27_prot_lipid.prm
> parameters ../c32b1/toppar/par_all27_na.prm
> parameters silicon_nitride.par
> paraTypeCharmm on
> exclude scaled1-4
> 1-4scaling 1
>
> switching on
> switchDist 10
> cutoff 12
> pairListDist 14
> #margin 2.5
>
> # integraion
> firsttimestep 14391000
> timestep 1
> nonBondedFreq 2
> fullElectFrequency 4
> stepsPerCycle 20
>
> # output
> binaryOutput yes
> binaryRestart yes
> wrapAll yes
> wrapNearest yes
> comMotion yes
>
> outputEnergies 1000
> outputPressure 1000
> outputTiming 1000
> xstFreq 1000
> dcdFreq 5000
> restartFreq 5000
>
> # electrostatics
> pme on
> pmeGridSizeX 192
> pmeGridSizeY 192
> pmeGridSizeZ 320
>
> # external forces
> constraints on
> consKCol B
> consRef ${sys}_restrain.pdb
> consKFile ${sys}_restrain.pdb
>
> gridforcechecksize off
> gridforce on
> gridforceFile specific.pdb
> gridforceCol B
> gridforceChargeCol O
> gridforcePotFile specific2-2.dx
> gridforceScale 2 2 2
> gridforceCont1 on
> gridforceCont2 on
> gridforceCont3 off
>
> set inStream [open $xsc r]
> set lengthZ [lindex [lindex [split [read $inStream] \n] 2] 9]
> close $inStream
> eFieldOn yes
> eField 0.0 0.0 [expr 23.06054917 * $voltage / $lengthZ]
>
> *******************************************************************************************
>
> The simulation has run for about 15 ns now and I do not see the DNA translocating in z-direction even a little bit. I had tried the tutorial with same model and parametes and under 20 V before and I could see it run perfectly. I do not ave any clue as to why I can't see the DNA move down the pore.
>
> Is there something I am doing wrong? I kindly request someone to look over this and guide me through fixing errors if I have any.
> **
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