From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Sep 13 2007 - 20:40:46 CDT
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
>>
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:15 CST