From: Philip Peartree (P.Peartree_at_postgrad.manchester.ac.uk)
Date: Fri Sep 14 2007 - 04:13:04 CDT
Apologies Peter! My bad!
Philip Peartree
Quoting Peter Freddolino <petefred_at_ks.uiuc.edu>:
> Hi Maria,
> you mentioned that you saw several atoms drift out of the box but
> maintain bonds to atoms in the box -- were you viewing the file using a
> pdb as the starting structure, or a psf? The most likely cause for what
> you're describing is just a visual artifact stemming from not using a
> structure file that includes bond information. Because atoms should only
> be wrapped across periodic boundaries as a complete bonded chain, you
> should not be getting bonds split across the periodic boundary.
>
> Out of curiosity, have you tried this run on the same hardware with a
> single processor? Stray PME grid charge errors are not possible with one
> processor, so this might help to find some underlying problem with the
> system. And have you performed other namd runs using the same
> computer(s) in the past?
>
> Wrapnearest effectively changes the shape of the unit cell you're using,
> and should be avoided unless you're certain that's what you want. It has
> no effect on a unit cell with orthogonal axes, but can be used to get
> unusual shapes (such as hexagonal cells) in other cases.
>
> Best,
> Peter
> Philip Peartree wrote:
>> 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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