Tutorial-l Mailing List

From: Athreya, Nagendra Bala Murali (nathreya_at_illinois.edu)
Date: Wed Nov 30 2016 - 20:46:29 CST

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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