AMBER Archive (2008)

Subject: AMBER: regarding segfault during energy minimization

From: Anamika Awasthi (aawasthi28_at_gmail.com)
Date: Wed Apr 30 2008 - 00:13:21 CDT

Dear Ross ,

 I used gcc compler and my machine is Linux AMD opteron based 64 bit archi
tecture and I am using serial envioronment.
This is output file--->

      -------------------------------------------------------
          Amber 9 SANDER 2006
          -------------------------------------------------------

| Run on 04/30/2008 at 11:25:34
  [-O]verwriting output

 Here is the input file:

rho:initial minimization with Cartesian restraints for the solute
&cntrl
imin=1, maxcyc=200,
ntpr=5,
ntr=1,
restraint_wt=50.0,
restraintmask=':1-1944',
/

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags:
 getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read

| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 53.237
| New format PARM file being parsed.
| Version = 1.000 Date = 04/28/08 Time = 17:03:16
 NATOM = 148533 NTYPES = 17 NBONH = 133395 MBONA = 15360
 NTHETH = 35322 MTHETA = 20712 NPHIH = 66444 MPHIA = 48360
 NHPARM = 0 NPARM = 0 NNB = 326426 NRES = 41249
 NBONA = 15360 NTHETA = 20712 NPHIA = 48360 NUMBND = 37
 NUMANG = 73 NPTRA = 43 NATYP = 29 NPHB = 1
 IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Memory Use Allocated
| Real 9593084
| Hollerith 932449
| Integer 5480366
| Max Pairs 49511000
| nblistReal 1782396
| nblist Int 6518026
| Total 332784 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

     BOX TYPE: TRUNCATED OCTAHEDRON

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
     imin = 1, nmropt = 0

Nature and format of input:
     ntx = 1, irest = 0, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 5, ntrx = 1, ntwr =
500
     iwrap = 0, ntwx = 0, ntwv = 0, ntwe
= 0
     ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0

Potential function:
     ntf = 1, ntb = 1, igb = 0, nsnb =
25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 0, ntr = 1

Energy minimization:
     maxcyc = 200, ncyc = 10, ntmin = 1
     dx0 = 0.01000, drms = 0.00010

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
     vdwmeth = 1, eedmeth = 1, netfrc = 0
     Box X = 130.403 Box Y = 130.403 Box Z = 130.403
     Alpha = 109.471 Beta = 109.471 Gamma = 109.471
     NFFT1 = 144 NFFT2 = 135 NFFT3 = 135
     Cutoff= 8.000 Tol =0.100E-04
     Ewald Coefficient = 0.34864
     Interpolation order = 4

    LOADING THE CONSTRAINED ATOMS AS GROUPS

   5. REFERENCE ATOM COORDINATES

     Mask :1-1944; matches 30630 atoms

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

 begin time read from input coords = 0.000 ps

 Number of triangulated 3-point waters found: 39299

     Sum of charges from parm topology file = -0.00000252
     Forcing neutrality...

--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------

 ---------------------------------------------------
 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 = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 27054460
| TOTAL SIZE OF NONBOND LIST = 27054460

   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 7.3878E+08 5.4632E+07 2.1205E+10 O 50311

 BOND = 635.4719 ANGLE = 3767.4121 DIHED =
18625.3499
 VDWAALS = ************* EEL = -509956.6162 HBOND =
0.0000
 1-4 VDW = 8179.5683 1-4 EEL = 79691.9336 RESTRAINT =
0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
      5 2.1616E+08 1.3622E+07 5.2885E+09 O 50311

 BOND = 635.6940 ANGLE = 3767.4299 DIHED =
18625.3509
 VDWAALS = ************* EEL = -509932.1931 HBOND =
0.0000
 1-4 VDW = 8179.5682 1-4 EEL = 79691.9342 RESTRAINT =
0.0180
 EAMBER = *************

   NSTEP ENERGY RMS GMAX NAME NUMBER
     10 2.2420E+07 6.0929E+05 2.0568E+08 O 50311

 BOND = 638.8230 ANGLE = 3767.6609 DIHED =
18625.3735
 VDWAALS = 22818599.3161 EEL = -509882.9377 HBOND =
0.0000
 1-4 VDW = 8179.5563 1-4 EEL = 79691.9499 RESTRAINT =
0.2667
 EAMBER = 22419619.7420

Hope, now you can understand my problem

Thanks in advance

 Anamika

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu