RE: constraint failure in Rattle algorithm for atom 54134

From: Tristan Croll (
Date: Mon Oct 26 2015 - 01:59:47 CDT

My guess here is that you need to include the line

regenerate angles dihedrals

at the end of your psfgen script (or choose this under the Options menu in AutoPSF). One of the many changes between CHARMM27 and CHARMM36 forcefields is that angles and dihedrals are no longer explicitly defined in patches, so without this line in your script any patch atoms will be bouncing around unrestrained (which, in my experience, typically leads to the below error in fairly short order).

From: [] On Behalf Of Life Sciences Inc
Sent: Monday, 26 October 2015 10:43 AM
Subject: namd-l: constraint failure in Rattle algorithm for atom 54134

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 (binary)
binvelocities $inputname.restart.vel # velocities from last run (binary)
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 completion

# Force-Field Parameters
paraTypeCharmm on # We're using charmm type parameter file(s)
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 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 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 PME
switchdist 10.0; # 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)
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 fftx/y/z
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 membrane
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 = 1.01325bar
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 period
langevinPistonTemp $temp; # coupled to heat bath

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

# run
run 50000000;

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