From: Athreya, Nagendra Bala Murali (nathreya_at_illinois.edu)
Date: Wed Nov 30 2016 - 21:20:55 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 parameters 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.
[On a side note: if I have multiple strands of DNA in the system, are there changes to the gridforcePotFile/gridforceFile to be made?]
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