AW: Fatal error..

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Jun 23 2014 - 03:33:27 CDT

What you see might just be the barostat being the 1st thing to break because of instability of your system. Possibly something is wrong with your carbon parameters. Try a low dcdfreq and see if you get some frames before it breaks to check visually what's going on.

Norman Geist.

> -----Urspr√ľngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Gurpreet Kaur Dhindsa
> Gesendet: Montag, 23. Juni 2014 00:32
> An: Namd Mailing List
> Betreff: namd-l: Fatal error..
>
> Dear All,
> I am running simulation contains carbon with water box. It showed me
> this error message
>
> 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.
>
> It stopped 2-3 times because water box was shrinking but now I looked
> at the
> water box size is good enough. I looked in the mailing list peopled had
> this problem
> but I didn't find in my conf file what I can change to get rid of that
> problem.
> Appreciate for your suggestions.
>
> Here is my configuration file
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> margin 2.5
> structure ../common/ND_water4.psf
> coordinates ../common/5ND_water.restart.pdb
>
> set temperature 300
> set outputname 5ND_water
>
> firsttimestep 0
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters ../common/par_all27_prot_na.prm
> temperature $temperature
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.0
> switching on
> switchdist 10.0
> pairlistdist 14.0
>
> # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 1/ps
> langevinTemp $temperature
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
>
> # Periodic Boundary Conditions
> cellBasisVector1 325.0 0.0 0.0
> cellBasisVector2 0.0 205.0 0.0
> cellBasisVector3 0.0 0.0 145.0
> cellOrigin -34.23 5.37 0.12
>
> wrapAll on
>
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSpacing 1.0
>
> #manual grid definition
> #PMEGridSizeX 45
> #PMEGridSizeY 45
> #PMEGridSizeZ 48
>
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes ;# needed for rigidBonds
> useFlexibleCell no
> useConstantArea no
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 100.0
> langevinPistonDecay 50.0
> langevinPistonTemp $temperature
>
>
> # Output
> outputName $outputname
>
> restartfreq 1000 ;# 1000steps = every 2ps
> dcdfreq 1000
> xstFreq 1000
> outputEnergies 1000
> outputPressure 1000
>
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> minimize 25000 ;# 50ps
> reinitvels $temperature
>
> run 3000000 ;# 6ns

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