Dear CHARMM users,

I am working on a system of approximatively 165000 atoms (from which, more than 120000 water atoms and ~320 ions (NaCl)).
I have a tetrahedral water box.
I would like to run a MD simulation on this system in periodic boundary conditions. I have just built my system and now I would like to minimise it.
But CHARMM crashes even before to start the minimisation with this error message:

NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec FSWItch VATOm VFSWIt
BYGRoup NOEXtnd EWALd
CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 13.000
WMIN = 1.400 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
PME EWALD OPTIONS: KAPPA = 0.380 QCOR = 0.000 Bspline order = 6
FFTX= 256 FFTY= 256 FFTZ= 128
Using Pub FFT
Real-to-Complex FFT
There are 0 atom pairs and 0 atom exclusions.
There are 0 group pairs and 0 group exclusions.
with mode 5 found 208230 exclusions and 65921 interactions(1-4)
found 15712 group exclusions.
VEHEAP> Expanding heap size by 966656 words.
found 0 image group exclusions.
Generating nonbond list with Exclusion mode = 5
VEHEAP> Expanding heap size by 4030464 words.
== PRIMARY == SPACE FOR 1439730 ATOM PAIRS AND 0 GROUP PAIRS

General atom nonbond list generation found:
1059303 ATOM PAIRS WERE FOUND FOR ATOM LIST
63076 GROUP PAIRS REQUIRED ATOM SEARCHES

SPACE FOR 418704 ATOM PAIRS AND 0 GROUP PAIRS

Image nonbond list generation found:
123152 ATOM PAIRS WERE FOUND FOR ATOM LIST
0 ATOM PAIRS WERE FOUND FOR ATOM SELF LIST
11002 GROUP PAIRS REQUIRED ATOM SEARCHES


***** LEVEL -4 WARNING FROM *****
***** Bad vdw option
******************************************


And here is my code:



! Read in Topology and Parameter files
open unit 1 card read name top_all27_prot_na.inp
read RTF card unit 1
close unit 1

open unit 1 card read name par_all27_prot_na.inp
read PARA card unit 1
close unit 1

open unit 13 file read name "solva.psf"
read psf file unit 13
close unit 13

open unit 14 file read name "solva.crd"
read coor file unit 14
close unit 14

open unit 15 card read name "200NaCl.crd"
read sequ coor unit 15
gene sel setup
rewind unit 15
read coor card unit 15 appe
close unit 15

open unit 16 card read name "126Na.crd"
read sequ coor unit 16
gene salt setup
rewind unit 16
read coor card unit 16 appe
close unit 16

DELE ATOM SELE (.BYRES.( SEGID SOLV .AND. (SEGID SEL .AROUND. 2.60))) END
DELE ATOM SELE (.BYRES.( SEGID FLOT .AND. (SEGID SEL .AROUND. 2.60))) END
DELE ATOM SELE (.BYRES.( SEGID EAUX .AND. (SEGID SEL .AROUND. 2.60))) END
DELE ATOM SELE (.BYRES.( SEGID WASS .AND. (SEGID SEL .AROUND. 2.60))) END

DELE ATOM SELE (.BYRES.( SEGID WATR .AND. (SEGID SEL .AROUND. 2.60))) END
DELE ATOM SELE (.BYRES.( SEGID AQUA .AND. (SEGID SEL .AROUND. 2.60))) END
DELE ATOM SELE (.BYRES.( SEGID EVIA .AND. (SEGID SEL .AROUND. 2.60))) END
DELE ATOM SELE (.BYRES.( SEGID FLOT .AND. (SEGID SALT .AROUND. 2.60))) END
DELE ATOM SELE (.BYRES.( SEGID EAUX .AND. (SEGID SALT .AROUND. 2.60))) END
DELE ATOM SELE (.BYRES.( SEGID WASS .AND. (SEGID SALT .AROUND. 2.60))) END
DELE ATOM SELE (.BYRES.( SEGID AQUA .AND. (SEGID SALT .AROUND. 2.60))) END
DELE ATOM SELE (.BYRES.( SEGID EVIA .AND. (SEGID SALT .AROUND. 2.60))) END
DELE ATOM SELE (.BYRES.( SEGID WATR .AND. (SEGID SALT .AROUND. 2.60))) END
DELE ATOM SELE (.BYRES.( SEGID SOLV .AND. (SEGID SALT .AROUND. 2.60))) END



OPEN WRITE CARD UNIT 41 NAME "ion_solva.pdb"
WRITE COOR PDB UNIT 41

!crystal symmetrie definition
crystal defi tetr 162.0 162.0 74.0 90.0 90.0 90.0
crystal build cutoff 15.5 nope 0 !nope: number of sym. operation
!Apply image centering to all molecules
image byres sele all end

!define energy and non-bond interactions
energy elec atom fswitch vdw vatom vfswitch cdie eps 1.0 -
CUTNB 14.0 CTONNB 10.0 CTOFNB 13.0 WMIN 1.4 -
cutim 15.0 imgfrq 20 inbfrq 10 -
ewald pmewald kappa 0.38 order 6 -
fftx 256 ffty 256 fftz 128 spline qcor 0.0

! do minimisation
mini sd nstep 5000 nprint 50 tolgrad 0.1 ixtfrq 50
mini conj nstep 10000 nprint 50 tolgrad 0.01 ixtfrq 50

OPEN WRITE CARD UNIT 41 NAME "mini_ion_solva_nuc.psf"
WRITE PSF CARD UNIT 41

OPEN WRITE CARD UNIT 41 NAME "mini_ion_solva_nuc.pdb"
WRITE COOR PDB UNIT 41

OPEN WRITE CARD UNIT 41 NAME "mini_ion_solva_nuc.crd"
WRITE COOR CARD UNIT 41

stop


I hope that I give here all the necessary information to get some answer elements.

Thanks a lot!

Karine