From: Markus K. Dahlgren (markus.dahlgren_at_yale.edu)
Date: Wed Apr 20 2011 - 09:30:11 CDT
Hi Ed,
I think the simplest way of getting around the RATTLE problem is to set your
timestep to 0.3-0.5 and run for a few 100k timesteps. Then switch back to 2fs
timestep. Usually this solves the problem, but I found RATTLE problems to be
too frequent on my systems so I usually run with a 1fs timestep and then you
wont see the RATTLE error.
/Markus
Quoting Edward Lyman <edward.lyman_at_gmail.com>:
> Hi all,
>
> I am simulating a bilayer with the charmm36 parameters, which was
> extensively minimized, heated, and relaxed. I find the simulation always
> crashes due to a rattle failure, typically between 4M and 8M timesteps.
> Nothing special in the cfg file except for the use of force-based switching,
> as required by the charmm36 parameterization. (details of the cfg below) I
> am wondering if anyone else has seen this issue?
>
> The only other thing that is out of the ordinary is that I am running the
> simulation on 176 procs, since that is what I have available. I plan to test
> and see if it is stable on a more normal partition, like 128, but a careful
> reading of the fft cfg section suggests 176 should be ok in NAMD.
>
> Any insights appreciated. The error and cfg below.
>
> Thx,
> Ed
>
> log file end:
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 20051000
> WRITING COORDINATES TO DCD FILE AT STEP 20051000
> WRITING COORDINATES TO RESTART FILE AT STEP 20051000
> FINISHED WRITING RESTART COORDINATES
> ERROR: Constraint failure in RATTLE algorithm for atom 15602!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Exiting prematurely; see error messages above.
> ====================================================
>
> WallClock: 68395.648438 CPUTime: 66929.414062 Memory: 244.082031 MB
>
>
>
> The relevant cfg sections:
>
> #******************************run parameters*****************************
> # number of steps set in FEP section
> firsttimestep 13800000
> numsteps 103800000
> timestep 2.0
> #temperature 310K #comment out when
> restarting
>
> #*****************************pressure control*****************************
> useGroupPressure yes
> useFlexibleCell yes
> useConstantRatio yes
> #useConstantArea no
> LangevinPiston on
> LangevinPistonTarget 1.01325
> LangevinPistonPeriod 500
> LangevinPistonDecay 100
> LangevinPistonTemp 310
>
> #******************************electrostatics******************************
> fullElectFrequency 1
> exclude scaled1-4
> 1-4scaling 1.0
> switching on
> vdwForceSwitching on
> switchdist 10.0
> cutoff 12.0
> pairlistdist 13.5
>
> #**********************************bonds***********************************
>
> rigidBonds all
> rigidTolerance 1.0e-5
> #
> #*******************************PME options********************************
> PME yes
> PMEPencils 1
>
> # New Style
> PMETolerance 1.0e-6
> PMEInterpOrder 6
> PMEGridSpacing 1.0
>
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