From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Mon Oct 26 2015 - 08:31:44 CDT
Hi there,
I have had this issue a few times. Could you tell me a bit about how you
built your structure, and what it has (i.e. peptide, lipid, water etc)?
Best,
Chitrak.
On Sun, Oct 25, 2015 at 8:42 PM, Life Sciences Inc <
contact.lifesciences.inc_at_gmail.com> wrote:
> 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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