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Dear amberers,
I'm trying to run sander_classic on an explicity hydrated system
(lysozyme), but the process stops suddenly giving the error:
.....
oct box min vector; 25.433 23.958
vlimit exceeded for step 0; vmax = 1111.04407
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
Npairs =26786207 Exceeds Max= 9000000
I could not find how to increase the 9000000 limit for NPAIRS, I tried
to increase the integer memory fron 2000000 to 32000000, that in
sander_classic.f is described as dependent upon NPAIRS, but had no
succsess. Does anyone know if such limit can be overcome and how?
Thanks in advance, Andrea.
PS: the full output follow below
______________________________________________
Andrea Bernini, Ph.D.
Molecular Biology Dept.
University of Siena
Via Fiorentina 1, 53100 Siena, Italy
-------------------------------------------------------
Amber 6 SANDER_CLASSIC Scripps/UCSF 1999
-------------------------------------------------------
| Thu Dec 13 15:17:31 2001
[-O]verwriting output
File Assignments:
|MDIN :
md1.in
|MDOUT:
md1.out
|INPCR:
min1.xyz
|PARM :
prmtop.wat
|RESTR:
md1.xyz
|REFC :
refc
|MDVEL:
mdvel
|MDEN :
mden
|MDCRD:
mdcrd
|MDINF:
mdinfo
Here is the input file:
#molecular
dynamics
&cntrl
imin=0, ntx=1, tempi=0,
init=3,
scee=1.2, idiel=1,
cut=11.0,
ntt=5, temp0=100.0,
tautp=0.05,
tauts=0.05,
vlimit=20,
ntp=2, taup=0.1,
imgslt=1,
ntb=2, ntc=3, ntf=3,
nsnb=10,
nstlim=1000,
dt=0.002,
ntwe=100, ntwx=100,
ntpr=100,
&end
-------------------------------------------------------------------------------
#molecular
dynamics
| Reading &cntrl namelist w/ machine lib
1. RESOURCE USE:
NATOM = 7322 NTYPES = 19 NBONH = 6296 MBONA = 1025
NTHETH = 2158 MTHETA = 1389 NPHIH = 3792 MPHIA = 1821
NHPARM = 0 NPARM = 0 NNB = 17874 NRES = 1933
NBONA = 1025 NTHETA = 1389 NPHIA = 1821 NUMBND = 53
NUMANG = 120 NPTRA = 69 NATYP = 31 NPHB = 1
IFBOX = 2 NMXRS = 24 IFCAP = 0
| Memory Use Allocated Used
| Real 3700000 263627
| Hollerith 600000 60511
| Integer 32000000 254184 (static)
| Max Nonbonded Pairs: 9000000 packed 2 to a machine word
BOX TYPE: TRUNCATED OCTAHEDRON
2. CONTROL DATA FOR THE RUN
LYSO
TIMLIM= 999999. IREST = 0 IBELLY= 0
KFORM = 1 ICHDNA= 0 IMIN = 0
IPOL = 0 IEWALD= 0
NTX = 1 NTXO = 1
IG = 71277 TEMPI = 0.00 HEAT = 0.000
NTB = 2 IFTRES= 1 BOXX = 67.503
BOXY = 51.705 BOXZ = 50.867
NRUN = 1 NTT = 5 TEMP0 = 100.000
DTEMP = 0.000 TAUTP = 0.050 TAUTS = 0.050
ISOLVP= 0 VLIMIT= 20.000
NTP = 2 PRES0 = 1.000 COMP = 44.600
TAUP = 0.100 NPSCAL= 0
NTCM = 0 NSCM = 9999999
NSTLIM= 1000 INIT = 3 NTU = 1
T = 0.000 DT = 0.00200
NTC = 3 TOL = 0.00050 JFASTW = 0
NTF = 3 NTID = 0 NTNB = 1
NSNB = 10 IDIEL = 1 IMGSLT= 1
IPRR = 0 IPRW = 0 ITRSLU= 1
CUT = 11.000 SCNB = 2.000
SCEE = 1.200 DIELC = 1.000
CUT2ND= 0.00000
NTPR = 100 NTWR = 50 NTWX = 100
NTWV = 0 NTWE = 100 NTWXM = 999999
NTWVM = 999999 NTWEM = 999999 IOUTFM= 0
NTWPRT= 0 NTWPR0= 0
NTR = 0 NTRX = 1
TAUR = 0.00000 NMROPT= 0 ISFTRP= 0
RWELL = 1.00000 PENCUT= 0.10000
IVCAP = 0 MATCAP= 0 FCAP = 1.500
IRDARC= 0 IRD1ST= 0 IRDLST= 0
IWRTSM= 0
OTHER DATA:
IFCAP = 0 NATCAP= 0 CUTCAP= 0.000
XCAP = 0.000 YCAP = 0.000 ZCAP = 0.000
NATOM = 7322 NRES = 1933
Water definition for fast triangulated model:
Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ; Hyd2_name = H2
GFTIM = 2.00000 RLMAVF= 0.00000 ISGDEP= 3
NMRAFA= 0 ILTAVF= 0
Ligand Grid: OFF (not requested)
3. ATOMIC COORDINATES AND VELOCITIES
LYSO
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 1779
Using 1779 waters for fast wat-wat
Solute/solvent pointers:
IPTSOL= 154 NATRCM= 1985
IPTRES= 0 IPTATM= 0
NSPSOL= 3 NSPSTR= 1985
NSOLUT= 1985 NATOM = 7322
oct box min vector; 25.433 23.958
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
oct box min vector; 25.433 23.958
NB-update: NPAIRS = 2336210 HBPAIR = 466716
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =2044881.46
Etot = 36285.8890 EKtot = 0.0000 EPtot = 36285.8890
BOND = 0.0000 ANGLE = 235.6236 DIHED = 697.2827
1-4 NB = 557.1223 1-4 EEL = 4018.3795 VDWAALS = 56405.5802
EELEC = -25628.0994 EHBOND = 0.0000 CONSTRAINT = 0.0000
EKCMT = 0.0000 VIRIAL = ************ VOLUME = 88768.4599
T_SOLUTE = 0.0000 T_SOLVENT = 0.0000
Density = 0.8820
------------------------------------------------------------------------------
oct box min vector; 25.433 23.958
vlimit exceeded for step 0; vmax = 1111.04407
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
oct box min vector; nan nan
Npairs =26786207 Exceeds Max= 9000000
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Received on Fri Dec 14 2001 - 01:12:56 PST
