From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Thu Sep 13 2007 - 08:39:46 CDT
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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