Re: Error while equilibrating AGNR nanopore + DNA system

From: Priyanka Mondal (pmondal_at_udel.edu)
Date: Mon Apr 15 2019 - 12:27:31 CDT

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> 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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