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#953 - 02/17/04 11:08 PM About the Script "run-pbc-md.inp "
label Offline
Forum Member

Registered: 12/30/03
Posts: 80
Dear all ,
I want to set the water box with volume "70*70*70 A**3".
And I modified the script "run-pbc-md.inp ".I chage the
command line and see above .I chaged the the value "16" to
the value "32". But a error message appeared .
Could you tell me how to fix my problem ? And I want to
add "NaCl " atoms to the water box. How could I get it ?
Thank you ...
Yeng tseng

Command lines in run-pbc-md.inp
******************************************************************
.....
calc XSIZ = INT( ?XMAX - ?XMIN + 16)
calc YSIZ = INT( ?YMAX - ?YMIN + 16)
calc ZSIZ = INT( ?ZMAX - ?ZMIN + 16)
....
************************************************************
modified command line
************************************************************
....
calc XSIZ = INT( ?XMAX - ?XMIN + 32)
calc YSIZ = INT( ?YMAX - ?YMIN + 32)
calc ZSIZ = INT( ?ZMAX - ?ZMIN + 32)
....
****************************************************************

error message
*****************************************************************
CHARMM> read sequence tip3 @NSLAB
Parameter: NSLAB -> "1944"

CHARMM> gene wat3 noangle nodihe
NO PATCHING WILL BE DONE ON THE FIRST RESIDUE
NO PATCHING WILL BE DONE ON THE LAST RESIDUE
GENPSF> Segment 5 has been generated. Its identifier is WAT3.
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 5 Number of residues = 8872
Number of atoms = 27304 Number of groups = 8946
Number of bonds = 27362 Number of angles = 10330
Number of dihedrals = 2160 Number of impropers = 66
Number of HB acceptors = 9024 Number of HB donors = 52
Number of NB exclusions = 0 Total charge = -22.00000
**** ERROR **** A COUNTER VARIABLE HAS EXCEEDED ITS MAXIMUM ALLOWABL
E VALUE.
EXECUTION WILL BE TERMINATED.
THE CURRENT COUNTER VARIABLES AND THEIR MAXIMUM ALLOWED VALUES A
RE:
NSEG = 5 MAXSEG = 5000 NATOM = 27304 MAXA =
30000 NBOND = 27362 MAXB = 30000
NTHETA = 10330 MAXT = 30000 NPHI = 2160 MAXP =
60000 NIMPHI = 66 MAXIMP = 9200
NNB = 0 MAXNB = 17200 NDON = 52 MAXPAD =
8160 NACC = 9024 MAXPAD = 8160
NRES = 8872 MAXRES = 14000 NATC = 107 MAXATC =
500 NCB = 119 MAXCB = 1500
NCT = 288 MAXCT = 15500 NCP = 611 MAXCP =
3000 NCI = 35 MAXCI = 600
NCH = 0 MAXCH = 3200 NCN = 3160 MAXCN =
20100
*** LEVEL -4 WARNING *** BOMLEV IS -2
BOMLEV HAS BEEN SATISFIED. TERMINATING.

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#954 - 02/18/04 02:31 AM Re: About the Script "run-pbc-md.inp " [Re: label]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4745
Loc: ~ 59N, 15E
As you can see from the error message your system contains too many possible hydrogen bond acceptors, and you may also end up with too many atoms; for a system this big you need to install CHARMM with at least the large option. The version you are currently using was installed with the medium option. Since you seem to be using CHARMm (rather than CHARMM) I am not sure how you select a large version of the program. If you cannot do this you may have to make do with only 8A between the solute and the boundary, which still leaves 16A between the solute and its image.
The issue about adding ions has been discussed a few months ago on this forum.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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