Dear Amber Users:
I'm using amber6 to carry out a simple minimization of Plastocyanin in
water following the tutorial at
http://amber.scripps.edu/tutorial/plastocyanin/pcy-tutorial-sh-3.html.
From the output, it seems MAX_RSTACK should be increased. So I modified
the size.h with the follwing parameters:
-----------
#ifndef MEM_ALLOC
parameter (MAXREA=20000000)
parameter (MAXINT=20000000)
parameter (MAXHOL=1000000)
parameter (MAXPR=30000000)
#endif
parameter (MAXDUP=1000)
integer MAX_RSTACK,MAX_ISTACK,MAX_STACK_PTRS,MAX_HEAP_PTRS
parameter (MAX_RSTACK=10000000)
parameter (MAX_ISTACK=10000000)
parameter (MAX_STACK_PTRS=100)
parameter (MAX_HEAP_PTRS=100)
-------------
and recompiled it with g77. But I still always get segmentation fault
when I run this minimization. I think the memory should be ok, right?
Attached is the output file and any suggestions will be very appreciated!
Regards!
Liu
-------------------------------------------------------
Amber 6 SANDER Scripps/UCSF 1999
-------------------------------------------------------
| Tue Mar 30 10:45:21 2004
[-O]verwriting output
File Assignments:
|MDIN : min2.in
|MDOUT: plc.min2.out
|INPCR: plc.wat.crd
|PARM : plc.wat.top
|RESTR: plc.rst
|REFC : refc
|MDVEL: mdvel
|MDEN : mden
|MDCRD: mdcrd
|MDINF: mdinfo
Here is the input file:
minimization
&cntrl
imin=1,
ntb=1, ntc=1,
maxcyc=500, ntpr=25,
&end
-------------------------------------------------------------------------------
minimization
1. RESOURCE USE:
getting box info from bottom of parm
getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
EWALD SPECIFIC INPUT:
-------------------------------------------------
NO EWALD INPUT FOUND: USING DEFAULTS
-------------------------------------------------
Largest sphere to fit in unit cell has radius = 27.984
Calculating ew_coeff from dsum_tol,cutoff
Box X = 58.230 Box Y = 63.857 Box Z = 55.969
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 60 NFFT2 = 64 NFFT3 = 60
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4
NATOM = 16255 NTYPES = 19 NBONH = 15502 MBONA = 763
NTHETH = 1628 MTHETA = 1040 NPHIH = 2933 MPHIA = 1866
NHPARM = 0 NPARM = 0 NNB = 27809 NRES = 5039
NBONA = 763 NTHETA = 1040 NPHIA = 1866 NUMBND = 37
NUMANG = 74 NPTRA = 27 NATYP = 29 NPHB = 1
IFBOX = 1 NMXRS = 22 IFCAP = 0
EWALD MEMORY USE:
| Total heap storage needed = 997
| Adjacent nonbond minimum mask = 27809
| Max number of pointers = 25
| List build maxmask = 55618
| Maximage = 23785
EWALD LOCMEM POINTER OFFSETS
| Real memory needed by PME = 997
| Size of EEDTABLE = 20918
| Real memory needed by EEDTABLE = 83672
| Integer memory needed by ADJ = 55618
| Integer memory used by local nonb= 875361
| Real memory used by local nonb = 266415
| MAX NONBOND PAIRS = 30000000
| Memory Use Allocated Used
| Real 20000000 1229435
| Hollerith 1000000 102571
| Integer 20000000 1225253
| Max Nonbonded Pairs:30000000
BOX TYPE: RECTILINEAR
2. CONTROL DATA FOR THE RUN
TIMLIM= 999999. IREST = 0 IBELLY= 0
IMIN = 1
IPOL = 0
NTX = 1 NTXO = 1
IG = 71277 TEMPI = 0.00 HEAT = 0.000
NTB = 1 BOXX = 58.230
BOXY = 63.857 BOXZ = 55.969
NTT = 0 TEMP0 = 300.000
DTEMP = 0.000 TAUTP = 1.000
VLIMIT= 0.000
NTP = 0 PRES0 = 1.000 COMP = 44.600
TAUP = 0.200 NPSCAL= 0
NTCM = 0 NSCM = 9999999
NSTLIM= 1 NTU = 1
T = 0.000 DT = 0.00100
NTC = 1 TOL = 0.00001 JFASTW = 0
NTF = 1 NSNB = 25
CUT = 8.000 SCNB = 2.000
SCEE = 1.200 DIELC = 1.000
NTPR = 25 NTWR = 50 NTWX = 0
NTWV = 0 NTWE = 0 IOUTFM= 0
NTWPRT= 0 NTWPR0= 0 NTAVE= 0
NTR = 0 NTRX = 1
TAUR = 0.00000 NMROPT= 0 PENCUT= 0.10000
IVCAP = 0 MATCAP= 0 FCAP = 1.500
OTHER DATA:
IFCAP = 0 NATCAP= 0 CUTCAP= 0.000
XCAP = 0.000 YCAP = 0.000 ZCAP = 0.000
VRAND= 0
NATOM = 16255 NRES = 5039
MAXCYC= 500 NCYC = 10 NTMIN = 1 DX0 = 0.010000
DXM = 0.50000 DRMS = 0.00010
Water definition for fast triangulated model:
Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ; Hyd2_name = H2
3. ATOMIC COORDINATES AND VELOCITIES
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 4931
Sum of charges from parm topology file = -0.00000005
Forcing neutrality...
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.3242E-14 at 2.436720
| CHECK d/dx switch(x): max rel err = 0.8156E-11 at 2.782960
---------------------------------------------------
Total number of mask terms = 22792
Total number of mask terms = 45584
| Total Ewald setup time = 0.08000004
------------------------------------------------------------------------------
NSTEP ENERGY RMS GMAX NAME NUMBER
1 3.1454E+20 4.1536E+20 5.5746E+22 N 1239
BOND = 7024.1947 ANGLE = 954.1097 DIHED = 560.6102
VDWAALS = ************* EEL = -54320.3184 HBOND = 0.0000
1-4 VDW = ************* 1-4 EEL = 6912.4118 CONSTRAINT = 0.0000
MAX_RSTACK in sizes.h and recompile
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Mar 30 2004 - 04:53:01 PST
