Re: Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected"

From: Philip Peartree (P.Peartree_at_postgrad.manchester.ac.uk)
Date: Thu Sep 13 2007 - 11:13:44 CDT

I think that using wrapNearest (i.e. setting wrapNearest to on) as well as
wrapAll might solve this problem... maybe others on the list can confirm this?

Phil Peartree

Quoting maria goranovic <mariagoranovic_at_gmail.com>:

> Hi,
>
> Yes, I am using full PBC. Below is the configuration script. The constraint
> file just has harmonic constraints (0.1) on all POPC atoms. Water is free
>
> #############################################3
> set MOL popc-big
>
> set xbox 114
> set ybox 114
> set zbox 168
>
> structure ${MOL}.psf
> coordinates ${MOL}.pdb
> temperature 0
> parameters par_all27_prot_lipid.prm
> paraTypeCharmm on
>
> outputEnergies 5000
> outputTiming 5000
> xstFreq 5000
> dcdFreq 5000
> wrapAll on
>
> timestep 1
> nonBondedFreq 1
> fullElectFrequency 1
> stepsPerCycle 20
>
> exclude scaled1-4
> 1-4scaling 1.0
> switching on
> switchDist 12
> cutoff 14
> pairlistdist 17
>
> cellBasisVector1 $xbox 00.00 00.00
> cellBasisVector2 00.00 $ybox 00.00
> cellBasisVector3 00.00 00.00 $zbox
>
> cellOrigin 0 0 0
>
> Pme on
> PmeGridsizeX 120
> PmeGridsizeY 120
> PmeGridsizeZ 180
>
> constraints on
> consRef ${MOL}-cons.pdb
> consKFile ${MOL}-cons.pdb
> consKCol B
>
> #########################################
> # PRESSURE AND TEMPERATURE CONTROL
> #########################################
>
> # temperature
> langevin on
> langevinDamping 5
> langevinTemp $temp
> langevinHydrogen no
>
> useflexiblecell yes
> useconstantratio yes
> langevinPiston on
> langevinPistonTarget 1.01325
> langevinPistonPeriod 100
> langevinPistonDecay 50
> langevinPistonTemp $temp
>
> binaryoutput on
> outputname ${MOL}-equil
>
> # INITIAL ENERGY
> minimize 0
>
> minimize 10000
> output ${MOL}-min1
>
> minimize 10000
> output ${MOL}-min2
>
> minimize 10000
> output ${MOL}-min3
>
> #########################################
> # HEAT WITH PC constrained
> #########################################
>
> set tem 1
> while { $tem <= 313 } {
> langevinTemp $tem
> run 3000
> output ${MOL}-heat-$tem
> set tem [expr $tem + 3]
> }
>
> run 100000
> output ${MOL}-dyna-1
> #############################################3
>
>
>
> On 9/13/07, Philip Peartree <P.Peartree_at_postgrad.manchester.ac.uk> wrote:
>>
>> I assume you're running in full periodic boundary conditions? Could you
>> post the
>> input script you're using?
>>
>> Philip Peartree
>>
>> Quoting maria goranovic <mariagoranovic_at_gmail.com>:
>>
>> > Hi,
>> >
>> > I have a 110 x 110 x 170 A bilayer (build using vmd plugins), which I am
>> > trying to minimize using a PME grid of 120 x 120 x 180. However,
>> starting
>> > from minimization step 80, I get several errors similar to the following
>> in
>> > the simulation
>> >
>> > ##############################
>> > ..
>> > ERROR: Stray PME grid charges detected: 28 sending to 25 for planes 92
>> 93 94
>> > 95
>> > ERROR: Stray PME grid charges detected: 28 sending to 10 for planes 36
>> 37 38
>> > 39
>> > ##############################
>> >
>> > Eventually the simulation crashes with the log:
>> >
>> > ##############################
>> > ..
>> >
>> > ERROR: Stray PME grid charges detected: 28 sending to 23 for planes 84
>> 85 86
>> > 87
>> > Stack Traceback:
>> > [0]
>> _ZN17ComputeHomeTuplesI8BondElem4bond9BondValueE10loadTuplesEv+0x95e
>> > [0x81311ae]
>> > [1] _ZN17ComputeHomeTuplesI8BondElem4bond9BondValueE6doWorkEv+0x56b
>> > [0x8133b7b]
>> > [2] _ZN11WorkDistrib12enqueueBondsEP12LocalWorkMsg+0x19 [0x82de0ed]
>> > [3]
>> >
>> _ZN19CkIndex_WorkDistrib31_call_enqueueBonds_LocalWorkMsgEPvP11WorkDistrib+0x11
>> > [0x82de0cd]
>> > [4] CkDeliverMessageFree+0x29 [0x8322f7d]
>> > [5] _Z15_processHandlerPvP11CkCoreState+0x417 [0x83225bf]
>> > [6] CmiHandleMessage+0x1d [0x837c885]
>> > [7] _ZN7BackEnd4initEiPPc+0x295 [0x80e2f89]
>> > [8] main+0x30 [0x80deff4]
>> > [9] __libc_start_main+0xdc [0xf7d3c87c]
>> > [10] _ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_c+0x59
>> > [0x80dba71]
>> > ##############################
>> >
>> > Looking at the trajectory (3 frames, 5000 steps of minimization each),
>> > several atoms have moved out of the simulation box, and have very long
>> bonds
>> > with atoms inside the box. These are both POPC and water atoms.
>> >
>> > Can someone please tell me what the issue might be ?
>> >
>> > Thank you very much,
>> > --
>> > Maria G.
>> > Technical University of Denmark
>> > Copenhagen
>> >
>>
>>
>>
>>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>

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