Error in NAMD Simulations -Drude

From: HEMANTH H 18310019 (hemanth.h_at_iitgn.ac.in)
Date: Mon Dec 24 2018 - 00:24:23 CST

I'm trying to perform an NPT simulation with Drude Polarizable model. The
simulation runs fine for some 720000 steps, after which the drudebond
temperature increases to 1.56 ( which otherwise is near 1.2), and the
simulation fails by flagging the error " ERROR: HardWallDrude> The drude is
too far away from atom 184 d = 0.505868!". The atom 184 is a nitrogen atom
on an adenine base.
please find the input file attached.
###############################################################################
structure final.psf
coordinates final.pdb
extendedSystem ./output/graph_ade_sheet_test-cpu-multi.1.xsc
binCoordinates ./output/graph_ade_sheet_test-cpu-multi.1.coor
binVelocities ./output/graph_ade_sheet_test-cpu-multi.1.vel

set temp 298;
set outputname ./output/graph_ade_sheet_test-cpu-multi.2;
binaryoutput yes;
binaryrestart yes;

outputEnergies 20000
outputPressure 20000
outputTiming 20000
xstFreq 20000
dcdFreq 20000
restartFreq 20000

#temperature $temp;
outputName $outputname; # base name for output from this run
                                # NAMD writes two files at the end, final
coord and vel
                                # in the format of first-dyn.coor and
first-dyn.vel

firsttimestep 0; # last step of previous run

#restartfreq 500; # 500 steps = every 1ps
#dcdfreq 1000;
dcdUnitCell yes; # the file will contain unit cell
info in the style of
                                       # charmm dcd files. if yes, the dcd
files will contain
                                       # unit cell information in the style
of charmm DCD files.
#xstFreq 1000; # XSTFreq: control how often the
extended systen configuration
                                       # will be appended to the XST file
#outputEnergies 250; # 250 steps = every 0.25ps
                                       # The number of timesteps between
each energy output of NAMD
#outputTiming 1000; # The number of timesteps between
each timing output shows
                                       # time per step and time to
completion

# Force-Field Parameters
# parameters
parameters ../toppar_drude/toppar_drude_master_protein_2013f.str;
parameters ../toppar_drude/toppar_drude_lipid_2017c.str;
parameters ../toppar_drude/toppar_drude_model_2013f.str;
parameters ../toppar_drude/toppar_drude_carbohydrate_2018a.str;
parameters ../toppar_drude/toppar_drude_nucleic_acid_2017c.str;
paratypecharmm on #
Type of Parameter File

# These are specified by CHARMM
exclude scaled1-4 # non-bonded exclusion policy to use
"none,1-2,1-3,1-4,or scaled1-4"
                                       # 1-2: all atoms pairs that are
bonded are going to be ignored
                                       # 1-3: 3 consecutively bonded are
excluded
                                       # scaled1-4: include all the 1-3,
and modified 1-4 interactions
                                       # electrostatic scaled by 1-4scaling
factor 1.0
                                       # vdW special 1-4 parameters in
charmm parameter file.
1-4scaling 1.0
switching on
vdwForceSwitching no; # force-based switching of vdW
should not be used for Drude FF
mergeCrossterms on

# You have some freedom choosing the cutoff
margin 3.0;
cutoff 9.0; # may use smaller, maybe 10., with PME
switchdist 8.0; # cutoff - 2.
                                       # switchdist - where you start to
switch
                                       # cutoff - where you stop accounting
for nonbond interactions.
                                       # correspondence in charmm:
                                       # (cutnb,ctofnb,ctonnb =
pairlistdist,cutoff,switchdist)
LJcorrection yes
pairlistdist 11.0; # stores the all the pairs with in
the distance it should be larger
                                       # than cutoff( + 2.)
stepspercycle 10; # 20 redo pairlists every ten steps
pairlistsPerCycle 2; # 2 is the default
                                       # cycle represents the number of
steps between atom reassignments
                                       # this means every 20/2=10 steps the
pairlist will be updated

# Integrator Parameters
timestep 1.0; # fs/step. If experiencing
instability, try smaller value, e.g., 0.75 or 0.5.
                                       # If drudeHardwall is not
applicable, please set 0.5.
rigidTolerance 0.000001;
rigidBonds all; # Bound constraint all bonds
involving H are fixed in length
nonbondedFreq 1; # nonbonded forces every step
fullElectFrequency 1; # PME every step

# Use Drude polarizable model
drude on
drudeTemp 1
drudeHardwall on # Only available in latest NAMD
(newer than 2.09). Please comment out this line in old namd.
drudeDamping 20.0
drudeBondLen 0.25 # Please set 0.20 if drudeHardwall
is not applicable.
drudeBondConst 40000
drudeNbtholeCut 5.0

#source step2_drude.str

# Periodic Boundary conditions. Need this since for a start...
#cellBasisVector1 $a 0.0 0.0; # vector to the next image
#cellBasisVector2 0.0 $b 0.0;
#cellBasisVector3 0.0 0.0 $c;
#cellOrigin $xcen $ycen $zcen; # the *center* of the cell
wrapWater on; # wrap water to central cell
wrapAll on; # wrap other molecules too
wrapNearest on; # use for non-rectangular cells
(wrap to the nearest image)
comMotion yes;

# PME (for full-system periodic electrostatics)
#exec python ./checkfft.py $a $b $c > ./checkfft.str
#source ./checkfft.str

PME yes;
PMEInterpOrder 6; # interpolation order (spline order
6 in charmm)
PMEGridSpacing 1.2;
#PMEGridSizeX $fftx; # should be close to the cell size
#PMEGridSizeY $ffty; # corresponds to the charmm input
fftx/y/z
#PMEGridSizeZ $fftz;

# Pressure and volume control
useGroupPressure yes; # use a hydrogen-group based
pseudo-molecular viral to calcualte pressure and
                                       # has less fluctuation, is needed
for rigid bonds (rigidBonds/SHAKE)
useFlexibleCell yes; # yes for anisotropic system like
membrane
useConstantArea yes;

langevin on
langevinDamping 1.0
langevinTemp $temp
langevinHydrogen off

# constant pressure
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 400.0
langevinPistonDecay 300.0
langevinPistonTemp $temp

# external forces
constraints on
consRef ./rest_graph_wat.pdb
consKFile ./rest_graph_wat.pdb
consKCol B

#colvars on
#colvarsConfig ../abf_3_15_ade.colvars

run 1000000

-- 
*Hemanth H 18310019*
Research Scholar
IIT Gandhinagar

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