From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Wed Apr 20 2011 - 09:50:37 CDT
turns out the issue has nothing to do with force switching, and everything
to do with some garbage that happened during the relaxation phase.
On Wed, Apr 20, 2011 at 10:30 AM, Markus K. Dahlgren <
markus.dahlgren_at_yale.edu> wrote:
> 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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