From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Mon Oct 26 2015 - 09:10:59 CDT
In case you still see the problem, you could also try to reduce the
timestep to 1fs for a while, and see if the error goes away. Another issue
could be heating it too rapidly, since you have lipids in your system.
Maybe try a gentler heating.
Best,
Chitrak.
On Mon, Oct 26, 2015 at 2:59 AM, Tristan Croll <tristan.croll_at_qut.edu.au>
wrote:
> 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:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *On
> Behalf Of *Life Sciences Inc
> *Sent:* Monday, 26 October 2015 10:43 AM
> *To:* namd-l_at_ks.uiuc.edu
> *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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