Re: Re: Error while equilibrating AGNR nanopore + DNA system

From: Victor Kwan (vkwan8_at_uwo.ca)
Date: Tue Apr 16 2019 - 06:02:50 CDT

Chances are your nanopore is not fixed. How did you set up the B/O column in your pdb file?

Regards,

Victor Kwan

On Mon, Apr 15, 2019 at 1:28 PM Priyanka Mondal <pmondal_at_udel.edu<mailto:pmondal_at_udel.edu>> wrote:
Here is my minimization and equilibration script :

*****************************************************************
*MINIMIZATION
*****************************************************************
set sys agnr_dna_sol
numsteps 2000
structure ${sys}_ions.psf
coordinates ${sys}_ions.pdb
outputName ${sys}_min
minimization on

# system dimensions
cellBasisVector1 151.04700028896332 0 0
cellBasisVector2 0 79.40799713134766 0
cellBasisVector3 0 0 137.07999801635742
cellOrigin 72.87791442871094 39.802154541015625 7.269594192504883

# parameters

#parameters ../../Packages/Force_Firlds_CHARMM/toppar/par_all27_na.prm
#parameters silicon_nitride.par


parameters ../../Packages/Force_Firlds_CHARMM/toppar/par_all36_prot.prm
parameters ../../Packages/Force_Firlds_CHARMM/toppar/toppar_water_ions.mod.str
parameters ../../Packages/Force_Firlds_CHARMM/toppar/par_all36_na.prm



paraTypeCharmm on
exclude scaled1-4
1-4scaling 1

switching on
switchDist 10
cutoff 12
pairListDist 14

# integraion
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 1000
restartFreq 1000

# electrostatics
#pme on
#pmeGridSizeX 96
#pmeGridSizeY 96
#pmeGridSizeZ 192

# external forces
constraints on
consKCol B
consRef harmonic_restrain.pdb
consKFile harmonic_restrain.pdb

gridforce on
gridforceFile dna_specific_f.pdb
gridforceCol B
gridforceChargeCol O
gridforcechecksize off
gridforcePotFile gra_specific.dx
gridforceScale 2 2 2
gridforceCont1 on
gridforceCont2 off
gridforceCont3 off



*****************************************************************
EQUILIBRATION
*****************************************************************
set sys agnr_dna_sol
set this ${sys}_eq
set last ${sys}_min

numsteps 600000
structure ${sys}_ions.psf
coordinates ${sys}_ions.pdb

outputName $this
binCoordinates $last.restart.coor
#binVelocities $last.restart.vel
temperature 295
extendedSystem $last.restart.xsc

# temperature control
langevin on

#run 1000
#for { set TEMP 1 } { $TEMP <= 290 } {incr TEMP 1 } {
#langevinTemp $TEMP
##langevinPistonTemp $TEMP
#}
#run 1000

langevinTemp 5

langevinFile agnr_dna_langevin.pdb
langevinCol B

# pressure control
useGroupPressure on
useFlexibleCell yes
useConstantArea yes
langevinPiston on
langevinPistonTarget 1.01325

langevinPistonTemp 5
langevinPistonDecay 1000
langevinPistonPeriod 2000

# parameters
parameters ../../Packages/Force_Firlds_CHARMM/toppar/par_all36_prot.prm
parameters ../../Packages/Force_Firlds_CHARMM/toppar/toppar_water_ions.mod.str
parameters ../../Packages/Force_Firlds_CHARMM/toppar/par_all36_na.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 20

# integraion
timestep 0.01
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 96
#pmeGridSizeY 96
#pmeGridSizeZ 192

# external forces
constraints on
consKCol B
consRef harmonic_restrain.pdb
consKFile harmonic_restrain.pdb

gridforce on
gridforceFile dna_specific_f.pdb
gridforceCol B
gridforceChargeCol O
gridforcechecksize off
gridforcePotFile gra_specific.dx
gridforceScale 2 2 2
gridforceCont1 on
gridforceCont2 off
gridforceCont3 off

************************************************************************************
Thank you for your attention.





Priyanka Mondal,
Department of Physics and Astronomy,
University of Delaware,
USA


On Mon, Apr 15, 2019 at 10:45 AM Priyanka Mondal <pmondal_at_udel.edu<mailto:pmondal_at_udel.edu>> wrote:
Hello all,
I am a beginner in NAMD and I am trying to simulate DNA through AGNR nanopore similar to tutorial DNA through Si3N4 in NAMD site. I have two questions.
First, the minimization ran without error but when I opened trajectory file, I saw the AGNR structure was distorted. I am not sure how to fix that. Quick google search suggested that I might have to define a force constant somewhere in parameter file. I am not sure how to do that.
  Secondly, I ran equilibration NAMD simulation anyway and there I encountered the error "Warning: Low global exclusion count!",
"ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on patch 58 pe 40).
"
and the simulation stops. I tried the following :
1> change langevinPistonTemp gradually so that there is gradual increase of force and thus limit velocity of atoms
2> Change timestep to much smaller values
But none of these seem to work. It will be nice if someone can help me. Thanks.


Priyanka Mondal,
Department of Physics and Astronomy,
University of Delaware,
USA

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