AMBER Archive (2008)

Subject: AMBER: (no subject)

From: Syed Tarique Moin (tarisyed_at_yahoo.com)
Date: Fri Feb 22 2008 - 00:10:36 CST

Hello,
   
  I am trying to minimize a complex, but i was stuck by the linmin error. I am attaching output file of minimization.
   
  Thanks in advance
   
  Regards

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

| Run on 02/22/2008 at 00:53:04
  [-O]verwriting output

File Assignments:
| MDIN: min500res.in
| MDOUT: min500res.out
|INPCRD: a_wat.inpcrd
| PARM: a_wat.prmtop
|RESTRT: min500res.restrt
| REFC: a_wat.inpcrd
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

 
 Here is the input file:
 
Minimization Amber9
 &cntrl
 imin=1, maxcyc=500,
 ntpr=5, ntr=1,
 &end
Restraints
 25.0
RES 1 633
END
END

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

| Flags: MPI
 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 = 41.112
| New format PARM file being parsed.
| Version = 1.000 Date = 02/21/08 Time = 16:43:42
 NATOM = 59490 NTYPES = 18 NBONH = 54486 MBONA = 5133
 NTHETH = 10821 MTHETA = 6970 NPHIH = 20811 MPHIA = 15935
 NHPARM = 0 NPARM = 0 NNB = 120143 NRES = 17214
 NBONA = 5133 NTHETA = 6970 NPHIA = 15935 NUMBND = 51
 NUMANG = 109 NPTRA = 50 NATYP = 34 NPHB = 1
 IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Memory Use Allocated
| Real 4071891
| Hollerith 374156
| Integer 2024999
| Max Pairs 2478750
| nblistReal 713880
| nblist Int 2496746
| Total 66196 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

     BOX TYPE: RECTILINEAR

--------------------------------------------------------------------------------
   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 = 500, 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 = 82.224 Box Y = 96.666 Box Z = 91.967
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 90 NFFT2 = 96 NFFT3 = 96
     Cutoff= 8.000 Tol =0.100E-04
     Ewald Coefficient = 0.34864
     Interpolation order = 4

    LOADING THE CONSTRAINED ATOMS AS GROUPS

   5. REFERENCE ATOM COORDINATES

      
    ----- READING GROUP 1; TITLE:
 Restraints

     GROUP 1 HAS HARMONIC CONSTRAINTS 25.00000
 GRP 1 RES 1 TO 633
      Number of atoms in this group = 9747
    ----- END OF GROUP READ -----

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

                                                                                
 begin time read from input coords = 0.000 ps

 Number of triangulated 3-point waters found: 16581
| Atom division among processors:
| 0 7436 14874 22308 29745 37182 44616 52053
| 59490

     Sum of charges from parm topology file = -0.32360874
     Assuming uniform neutralizing plasma
| Running AMBER/MPI version on 8 nodes

--------------------------------------------------------------------------------
   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 = 0.8314E-11 at 2.736960
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 1405134
| TOTAL SIZE OF NONBOND LIST = 10336257

   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 5.7364E+17 1.5567E+17 3.1549E+19 CA 3075

 BOND = 243646.1205 ANGLE = 4100.3728 DIHED = 5846.6820
 VDWAALS = ************* EEL = -204516.9558 HBOND = 0.0000
 1-4 VDW = ************* 1-4 EEL = 31395.6529 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
      5 3.7073E+16 8.0072E+15 1.6163E+18 CA 3075

 BOND = 243654.1386 ANGLE = 4101.4930 DIHED = 5846.8190
 VDWAALS = ************* EEL = -204516.5915 HBOND = 0.0000
 1-4 VDW = ************* 1-4 EEL = 31125.5931 RESTRAINT = 0.0180
 EAMBER = *************

   NSTEP ENERGY RMS GMAX NAME NUMBER
     10 1.4566E+14 1.9825E+13 4.0017E+15 CA 3075

 BOND = 243680.8699 ANGLE = 4105.7876 DIHED = 5847.3354
 VDWAALS = ************* EEL = -204515.5826 HBOND = 0.0000
 1-4 VDW = ************* 1-4 EEL = 30736.0821 RESTRAINT = 0.2704
 EAMBER = *************

     .... RESTARTED DUE TO LINMIN FAILURE ...

   NSTEP ENERGY RMS GMAX NAME NUMBER
     15 3.5900E+13 4.3453E+12 8.7713E+14 CA 3075

 BOND = 243691.0310 ANGLE = 4107.5708 DIHED = 5847.5505
 VDWAALS = ************* EEL = -204515.2549 HBOND = 0.0000
 1-4 VDW = ************* 1-4 EEL = 30663.0602 RESTRAINT = 0.4214
 EAMBER = *************

     .... RESTARTED DUE TO LINMIN FAILURE ...

   NSTEP ENERGY RMS GMAX NAME NUMBER
     20 3.5782E+13 4.3299E+12 8.7401E+14 CA 3075

 BOND = 243691.0571 ANGLE = 4107.5755 DIHED = 5847.5511
 VDWAALS = ************* EEL = -204515.2541 HBOND = 0.0000
 1-4 VDW = ************* 1-4 EEL = 30662.8983 RESTRAINT = 0.4219
 EAMBER = *************

     .... RESTARTED DUE TO LINMIN FAILURE ...

   NSTEP ENERGY RMS GMAX NAME NUMBER
     25 3.5664E+13 4.3144E+12 8.7089E+14 CA 3075

 BOND = 243691.0832 ANGLE = 4107.5801 DIHED = 5847.5517
 VDWAALS = ************* EEL = -204515.2533 HBOND = 0.0000
 1-4 VDW = ************* 1-4 EEL = 30662.7366 RESTRAINT = 0.4223
 EAMBER = *************

     .... RESTARTED DUE TO LINMIN FAILURE ...

   NSTEP ENERGY RMS GMAX NAME NUMBER
     30 3.5547E+13 4.2991E+12 8.6779E+14 CA 3075

 BOND = 243691.1093 ANGLE = 4107.5848 DIHED = 5847.5522
 VDWAALS = ************* EEL = -204515.2524 HBOND = 0.0000
 1-4 VDW = ************* 1-4 EEL = 30662.5750 RESTRAINT = 0.4227
 EAMBER = *************

     .... RESTARTED DUE TO LINMIN FAILURE ...

     ***** REPEATED LINMIN FAILURE *****

     ***** SEE http://amber.scripps.edu/Questions/linmin.html FOR MORE INFO *****

                    FINAL RESULTS

   NSTEP ENERGY RMS GMAX NAME NUMBER
     31 3.5509E+13 4.2941E+12 8.6680E+14 CA 3075

 BOND = 243691.1177 ANGLE = 4107.5863 DIHED = 5847.5524
 VDWAALS = ************* EEL = -204515.2522 HBOND = 0.0000
 1-4 VDW = ************* 1-4 EEL = 30662.5229 RESTRAINT = 0.4228
 EAMBER = *************

--------------------------------------------------------------------------------
   5. TIMINGS
--------------------------------------------------------------------------------

| Read coords time 0.09 ( 0.19% of Total)
| Fast Water setup 0.01 ( 0.01% of Total)
| Build the list 0.74 (53.93% of List )
| Other 0.63 (46.07% of List )
| List time 1.36 ( 3.89% of Nonbo)
| Short_ene time 14.01 (90.69% of Direc)
| Other 1.44 ( 9.31% of Direc)
| Direct Ewald time 15.45 (45.85% of Ewald)
| Adjust Ewald time 0.07 ( 0.21% of Ewald)
| Fill Bspline coeffs 0.70 ( 4.34% of Recip)
| Fill charge grid 0.73 ( 4.56% of Recip)
| Scalar sum 0.43 ( 2.67% of Recip)
| Grad sum 0.44 ( 2.71% of Recip)
| FFT back comm time 9.35 (74.85% of FFT t)
| Other 3.14 (25.15% of FFT t)
| FFT time 12.50 (77.90% of Recip)
| Other 1.25 ( 7.82% of Recip)
| Recip Ewald time 16.04 (47.59% of Ewald)
| Force Adjust 1.60 ( 4.76% of Ewald)
| Virial junk 0.53 ( 1.58% of Ewald)
| Ewald time 33.70 (96.11% of Nonbo)
| Nonbond force 35.07 (80.14% of Force)
| Bond/Angle/Dihedral 0.22 ( 0.51% of Force)
| FRC Collect time 4.22 ( 9.64% of Force)
| Other 4.25 ( 9.71% of Force)
| Force time 43.76 (100.0% of Runmd)
| Runmd Time 43.76 (92.34% of Total)
| Other 3.54 ( 7.46% of Total)
| Total time 47.39 (100.0% of ALL )

| Highest rstack allocated: 588891
| Highest istack allocated: 12393
| Job began at 00:53:04.366 on 02/22/2008
| Setup done at 00:53:07.437 on 02/22/2008
| Run done at 00:53:51.754 on 02/22/2008
| wallclock() was called 1374 times

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