constraint failure in Rattle algorithm for atom 54134

From: Life Sciences Inc (
Date: Sun Oct 25 2015 - 19:42:57 CDT

Dear All

I am trying to run the simulation but I am getting this error of constraint
failure in Rattle algorithm for atom 54134!

I am loading the psf with my trajectory and the structure seems goods, also
viewed the psf with last restart.coor file and everything seems fine. I
have also minimized the structure with 10,000 steps and then reran the
simulation but I got the same error on some other atom 40324. In my view
this is not the error of bad structure, if anyone has faced the similiar
problem and can get me out of this error, I will be really greatful.

This is my Configuration File

structure noclash_final.psf
coordinates noclash_final.pdb

set temp 303.15
outputName NPT_Prod_F3S # 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
set inputname NPT_Prod_F2
bincoordinates $inputname.restart.coor # coordinates from last run
binvelocities $inputname.restart.vel # velocities from last run
extendedSystem $inputname.restart.xsc # cell dimensions from
last run (binary)
restartfreq 50000 # 500 steps = every 1ps
dcdfreq 2500
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 2500 # XSTFreq: control how often the
extended systen configuration
                                       # will be appended to the XST file
outputEnergies 2500 # 125 steps = every 0.25ps
                                       # The number of timesteps between
each energy output of NAMD
outputTiming 2500 # The number of timesteps between
each timing output shows
                                       # time per step and time to

# Force-Field Parameters
paraTypeCharmm on # We're using charmm type parameter
parameters fluorophore.prm
parameters par_all36_cgenff.prm
parameters par_all36_lipid.prm
parameters par_all36_prot.prm

# 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
                                       # 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 yes; # New option for force-based
switching of vdW
                                       # if both switching and
vdwForceSwitching are on CHARMM force
                                       # switching is used for vdW forces.

# You have some freedom choosing the cutoff
cutoff 12.0; # may use smaller, maybe 10., with
switchdist 10.0; # cutoff - 2.
                                       # switchdist - where you start to
                                       # cutoff - where you stop accounting
for nonbond interactions.
                                       # correspondence in charmm:
                                       # (cutnb,ctofnb,ctonnb =
pairlistdist 14.0; # stores the all the pairs with in
the distance it should be larger
                                       # than cutoff( + 2.)
stepspercycle 20; # 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 2.0; # fs/step
rigidBonds all; # Bound constraint all bonds
involving H are fixed in length
nonbondedFreq 2; # nonbonded forces every step
fullElectFrequency 4; # PME every step

# Periodic Boundary conditions
cellBasisVector1 118.431 0. 0. ;# vector to the next image
cellBasisVector2 0. 118.431 0.
cellBasisVector3 0. 0 90.6448
cellOrigin 0.98007694 -0.51859881 -1.1731613 ;# the *center* of
the cell

wrapWater off; # wrap water to central cell
wrapAll off; # wrap other molecules too
wrapNearest off; # use for non-rectangular cells
(wrap to the nearest image)

# PME (for full-system periodic electrostatics)
#source checkfft.str

PME yes;
PMEInterpOrder 6; # interpolation order (spline order
6 in charmm)
PMEGridSizeX 125; # should be close to the cell size
PMEGridSizeY 125; # corresponds to the charmm input
PMEGridSizeZ 100;

#Constant Pressure Control (variable volume)
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
useConstantRatio yes; # keeps the ratio of the unit cell
in the x-y plane constant A=B

langevinPiston on; # Nose-Hoover Langevin piston
pressure control
langevinPistonTarget 1.01325; # target pressure in bar 1atm =
langevinPistonPeriod 2000.0; # oscillation period in fs.
correspond to pgamma T=50fs=0.05ps
                                       # f=1/T=20.0(pgamma)
langevinPistonDecay 1000.0; # oscillation decay time. smaller
value correspons to larger random
                                       # forces and increased coupling to
the Langevin temp bath.
                                       # Equall or smaller than piston
langevinPistonTemp $temp; # coupled to heat bath

# Constant Temperature Control
langevin on; # langevin dynamics
langevinDamping 1.0; # damping coefficient of 1/ps (keep
langevinTemp $temp; # random noise at this level
langevinHydrogen off; # don't couple bath to hydrogens

# run
run 50000000;

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