Re: Stray PME grid charges detected

From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Mon Apr 04 2016 - 13:02:51 CDT

Hi,

Thank you for the useful comments. I made the changes you said and started
a new simulation, and I am waiting for the result. However, I have a
question! Is that possible this error caused by the starting configuration?
Because it is a hyperbranched polymer.

Regards,
Farideh

On Mon, Apr 4, 2016 at 6:26 AM, Sourav Ray <souravrayiitkgp_at_gmail.com>
wrote:

> Hello
>
> 1. I think the timestep is too small (0.1 fs, usually 1 fs is minimum that
> is employed). Please confirm from previous literature.
> 2. Use a higher langevin damping constant for the thermostat, like say
> 10/ps, it solves a lot of issues during equilibration/relaxation.
> 3. If constant pressure is not working, either increase the margin from
> default 0 to say 5 or turn the flexible cell and constant area option on.
> You may need to turn both on initially, later remove the margin but keep
> flexible cell option on during production run.
> 4. I would suggest not to use unit cell dimensions larger than system
> size, it leads to density fluctuations at the corners of the cuboid.
> 5. TIme step x Number of steps = Total time, the output frequencies don't
> make sense to me.
> 6. Try rigidbond - hydrogen (or all) and check if there is any change.
>
> Regards
> Sourav
>
> On Sun, Apr 3, 2016 at 11:19 PM, faride badalkhani <
> farideh.khamseh_at_gmail.com> wrote:
>
>> Dear NAMD experts,
>>
>> I am going to run a minimization and NVT simulation followed by a NPT on
>> a system consists of a hyperbranched polymer in water. But, I got this
>> error:
>> atoms moving too fast simulation has become unstable NAMD
>> therefore, based on NAMD mailing list I increase the cellbasisvectorX, Y,
>> and Z size and decreased the time step to 0.1 but this time I got this
>> error:
>>
>> ERROR: Stray PME grid charges detected: 2 sending to 9 for planes 32 33
>> 34 35
>> ERROR: Margin is too small for 1 atoms during timestep 201933.
>> ERROR: Incorrect nonbonded forces and energies may be calculated!
>> FATAL ERROR: Low global CUDA exclusion count! (27955 vs 27959) System
>> unstable or pairlistdist or cutoff too small.
>>
>> FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
>> [0] Stack Traceback:
>> [0:0] CmiAbort+0x41 [0xefde44]
>> [0:1] _Z8NAMD_bugPKc+0x9e [0x64a77e]
>> [0:2] _ZN10Controller16compareChecksumsEii+0x86f [0x94db2f]
>> [0:3] _ZN10Controller9integrateEi+0xc8d [0x952e4d]
>> [0:4] _ZN10Controller9algorithmEv+0x1b2b [0x944f6b]
>> [0:5] CthStartThread+0x20 [0xef9e90]
>> [0:6] [0x33af8438f0]
>> [0] Stack Traceback:
>> [0:0] LrtsAbort+0x70 [0xefe524]
>> [0:1] CmiAbortHelper+0x102 [0xefddfd]
>> [0:2] CmiAbort+0x41 [0xefde44]
>> [0:3] _Z8NAMD_bugPKc+0x9e [0x64a77e]
>> [0:4] _ZN10Controller16compareChecksumsEii+0x86f [0x94db2f]
>> [0:5] _ZN10Controller9integrateEi+0xc8d [0x952e4d]
>> [0:6] _ZN10Controller9algorithmEv+0x1b2b [0x944f6b]
>> [0:7] CthStartThread+0x20 [0xef9e90]
>> [0:8] [0x33af8438f0]
>> I do not know what should I do now! Any help will be appreciated.
>>
>> My configuratyion file is as follows:
>>
>> # Input
>> paraTypeCharmm on
>> parameters G5-OH/par_all36_prot.prm
>> parameters G5-OH/par_all36_polyester.prm
>> temperature $temperature
>>
>>
>> # Force-Field Parameters
>> exclude scaled1-4 ;# These are specified by CHARMM
>> 1-4scaling 1.0 ;# These are specified by CHARMM
>> cutoff 12.0 ;# may use smaller, maybe 10.0, with PME
>> switching on
>> switchdist 10.0 ;# cutoff - 2.0
>> pairlistdist 14.0 ;# Promise that atom won’t move more than
>> 2A in a cycle, cutoff + 2
>>
>>
>> # Integrator Parameters
>> timestep 0.1 ;# 0.1fs/step
>> rigidBonds water
>> nonbondedFreq 1 ;# nonbonded forces every step
>> fullElectFrequency 2 ;# PME only every other step
>> stepspercycle 10 ;# redo pairlists every ten steps
>>
>>
>> # Constant Temperature Control
>> langevin on ;# langevin dynamics
>> langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
>> langevinTemp $temperature
>> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>>
>>
>> # Periodic Boundary Conditions
>> cellBasisVector1 42.00 0.00 0.00 ;# vector to the next image
>> cellBasisVector2 0.00 62.00 0.00
>> cellBasisVector3 0.00 0.00 40.00
>> cellOrigin -12.08 -1.14 -15.83 ;# the *center* of the cell
>>
>> wrapWater on ;# wrap water to central cell
>> wrapAll on ;# wrap other molecules too
>> wrapNearest off ;# use for non-rectangular cells
>>
>> # PME (for full-system periodic electrostatics)
>> PME yes
>> PMEGridSpacing 1.0
>>
>>
>> # Constant Pressure Control (variable volume)
>> useGroupPressure yes ;# needed for rigidBonds
>> useFlexibleCell no ;# no for water box, yes for membrane
>> useConstantArea no ;# no for water box, maybe for membrane
>>
>>
>> # Output
>> outputName $outputname
>>
>> restartfreq 500 ;# 500steps = every 1ps
>> dcdfreq 250
>> xstFreq 250
>> outputEnergies 100
>> outputPressure 100
>> outputTiming 1000 ;# shows time per step and time to completion
>>
>> #############################################################
>> ## EXTRA PARAMETERS ##
>> #############################################################
>>
>>
>> #############################################################
>> ## EXECUTION SCRIPT ##
>> #############################################################
>>
>> # Minimization
>> minimize 200000
>> reinitvels $temperature
>>
>> run 3000000 ;# 0.3 ns
>>
>> Truly yours,
>> Farideh
>>
>>
>

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