Re: Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step?

From: Elia Zumot (enz1+_at_pitt.edu)
Date: Wed Sep 09 2009 - 10:40:29 CDT

Hi Bjoern,

I work with membrane proteins and run into the same problem when I'm using
a 2 fs timestep (even though I set the rigidbonds to all). Have you tried
running at 1 fs?

Best

Elia

> Hi everyone,
>
> 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?
> 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
>
>

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