From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat Aug 11 2007 - 15:10:52 CDT
Hi Hsing,
you may want to try a simulation where you write a dcd every timestep,
so that you can see what is happening. When this error occurs in the
middle of the simulation it usually means that either you have atoms
flying off into space, or that your periodic cell shrank significantly
due to the barostat (which can happen, for example, if you have a poorly
equilibrated system). You should view your trajectory to see which is
happening here.
Also, are you sure you want to be using wrapnearest? That option should
only be used for non-parallelepiped unit cells.
Peter
Hsing Pao wrote:
> Hi everyone. Right now I am getting this error message when I try
> equilibration.
> Here's my error message:
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> ERROR: Margin is too small for 156 atoms during timestep 5.
> ERROR: Incorrect nonbonded forces and energies may be calculated!
> FATAL ERROR: Periodic cell has become too small for original patch grid!
> Possible solutions are to restart from a recent checkpoint,
> increase margin, or disable useFlexibleCell for liquid simulation.
>
> And here's my NAMD script file:
>
> set inpname 1JSO-pH-apo-salt-min_4
> set outname 1JSO-pH-apo-salt_eq_1
> firsttimestep 0
>
> # input
> amber yes
> parmfile 1JSO-pH-apo-salt.prmtop
> ambercoor 1JSO-pH-apo-salt.inpcrd
> readexclusions yes
> BinCoordinates $inpname.restart.coor
> #BinVelocities $inpname.restart.vel
> ExtendedSystem $inpname.xsc
>
> # Harmonic constraint part
> constraints on
> consRef restrain_backbone_ref.pdb
> consKFile restrain_backbone_ref.pdb
> consKCol O
> constraintScaling 1.0
>
> # force field parameters
> exclude scaled1-4
> 1-4scaling 0.833333
> cutoff 18
> switching On
> switchdist 12
> pairlistdist 20
> margin 2.5
>
> rigidBonds all
> rigidTolerance 0.0005
>
> # integrator params
> timestep 2.0
> numsteps 5000000
> nonbondedFreq 2
> PME yes
> PMEGridSizeX 70
> PMEGridSizeY 86
> PMEGridSizeZ 156
> FullElectFrequency 2
> stepspercycle 20
> langevin on # do langevin dynamics
> #langevinFile tempfile.pdb
> #langevinCol O
> langevinTemp 300.15 # bath temperature
> langevinDamping 5 # damping coefficient (gamma) of 5/ps
> langevinHydrogen no # don't couple langevin bath to hydrogens
> temperature 300.15
>
> # Pressure Control for NPT ensemble
> useFlexibleCell no
> langevinPiston on
> langevinPistonTarget 1.01325 # in bar -> 1 atm
> langevinPistonPeriod 100
> langevinPistonDecay 50
> langevinPistonTemp 300.15
>
> #PBC
> #cellBasisVector1 67.705 0.0 0.0
> #cellBasisVector2 0.0 82.089 0.0
> #cellBasisVector3 0.0 0.0 153.304
> #cellOrigin 34.991 42.629 78.834
> wrapWater on
> wrapAll on
> wrapNearest on
> xstFile $outname.xst
> xstFreq 10000
>
> # output
> outputname $outname
> dcdfile $outname.dcd
> restartname $outname.restart
> restartfreq 500
> dcdfreq 500
> binaryoutput yes
> outputEnergies 500
>
> I am not quite sure how to fix this problem. I have tried increasing
> the margin and increasing the PME grid size.
>
> Thanks,
>
> Hsing
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