From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Sep 09 2009 - 09:51:42 CDT
On Tue, 2009-09-08 at 10:12 +0200, Bjoern Olausson wrote:
> Hi everyone,
hi bjoern,
> it is some kind of strange to me what's going on here.
>
> I have a membrane NPGT simulations which crashes irregularly.
>
> The simulation was running fine for Xns (divided into 1ns runs) the Nth run
> crashed with "ERROR: Constraint failure in RATTLE algorithm for atom 6091!" at
> Step 16193900. Okay, no big deal so far. I run the Nth run again (from the
> restart files of the previous successful run). It crashed again with "ERROR:
> Constraint failure in RATTLE algorithm for atom 39616!" at Step 16337300.
> Now it made it over the previous crash point and failed on another timestep
> and another atom. Rerunning the Nth run a third time (again from the restart
> files of the previous successful run) it successfully completed.
>
> Now my question:
> Shouldn't the Simulation crash in all three runs at the same position an atom?
not necessarily. please keep in mind, that you are running with a
langevin thermostat that introduces some randomnes. if you are running
in parallel, you also have the load balancing that will redistribute
atoms sometimes differently. in general, MD trajectories tend to diverge
exponentially.
the real reason for the crashes have to be related, between the
individual runs. have you tried to look up what kind of atom
(most likely in a water molecule) is having the trouble. if you
get shake/rattle constraint failures, that is usually a sign for too
large forces and resulting too large displacements/acceleration
for shake/rattle to converge. that in turn can have three reasons,
your system is far from equilibrium, your parametrization is bad
somewhere, or your time step is too large for a system with such
steep potentials.
cheers,
axel.
> Is there some random seed which causes the above behaviour? Cause I would have
> expected the simulation to crash at the same point because all three runs were
> started from the same restart files?
>
> Here's my input file for the restart runs of my NPGT simulation:
> (best viewed with fixed font)
> -----------------------------------------------------------------------------
> structure step5_assembly.xplor.psf
> coordinates step6.6_equilibration.pdb
>
> set temp 303
> set outputname memb1_90
>
> firsttimestep 16000000
>
> # Input
> set inputname memb1_90
> binCoordinates run031/$inputname.restart.coor
> binVelocities run031/$inputname.restart.vel
> extendedSystem run031/$inputname.restart.xsc
> paraTypeCharmm on
> parameters par_all27_prot_lipid.prm
> parameters toppar_all27_lipid_cholesterol.str
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.0
> switching on
> switchdist 10.0
> pairlistdist 18
> pairlistsPerCycle 2
>
> # Integrator Parameters
> timestep 2.0
> rigidBonds all
> nonbondedFreq 1
> fullElectFrequency 1
> stepspercycle 10
>
> # Constant Temperature Control
> langevin on
> langevinDamping 5
> langevinTemp $temp
> langevinHydrogen off
>
> # Periodic Boundary Conditions
> cellBasisVector1 90.8625 0. 0.
> cellBasisVector2 0. 90.8625 0.
> cellBasisVector3 0. 0. 60.
> cellOrigin 0. 0. 0.
> wrapAll on
>
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSpacing 1.0
> #PMEGridSizeX 96
> #PMEGridSizeY 96
> #PMEGridSizeZ 60
>
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes
> useConstantArea no
> useConstantRatio no
> LangevinPiston on
> LangevinPistonTarget 1.01325
> LangevinPistonPeriod 200
> LangevinPistonDecay 100
> LangevinPistonTemp $temp
>
> SurfaceTensionTarget 1
>
> # Output
> outputName $outputname
>
> restartfreq 500
> dcdfreq 500
> xstFreq 500
> outputEnergies 100
> outputPressure 100
>
> run 500000
> -----------------------------------------------------------------------
>
> Kind regards
> Bjoern
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com Research Associate Professor Institute for Computational Molecular Science College of Science and Technology Temple University, Philadelphia PA, USA.
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