-------------------------------------------------------
          Amber 12 SANDER                              2012
          -------------------------------------------------------

| PMEMD implementation of SANDER, Release 11

| Run on 06/21/2011 at 13:14:53

| WARNING: Stack usage limited by a hard resource limit of  536870912 bytes!
|          If segment violations occur, get your sysadmin to increase the limit.
  [-O]verwriting output

File Assignments:
|   MDIN: mdin                                                                  
|  MDOUT: mdout.dhfr.CPU                                                        
| INPCRD: md12.x                                                                
|   PARM: prmtop                                                                
| RESTRT: restrt                                                                
|   REFC: refc                                                                  
|  MDVEL: mdvel                                                                 
|   MDEN: mden                                                                  
|  MDCRD: mdcrd                                                                 
| MDINFO: mdinfo                                                                


 Here is the input file:

 short md, nve ensemble                                                        
 &cntrl                                                                        
   ntx=7, irest=1,                                                             
   ntc=2, ntf=2, tol=0.0000001,                                                
   nstlim=20, ntt=0,                                                           
   ntpr=1, ntwr=10000,                                                         
   dt=0.001,                                                                   
 /                                                                             
 &ewald                                                                        
  NFFT1=72,NFFT2=64,NFFT3=60,                                                  
 /                                                                             


 
 
| Conditional Compilation Defines Used:
| DIRFRC_COMTRANS
| DIRFRC_EFS
| DIRFRC_NOVEC
| PUBFFT
| FFTLOADBAL_2PROC
| BINTRAJ
| MKL

| Largest sphere to fit in unit cell has radius =    27.261

|  INFO: Old style PARM file read


| Note: 1-4 EEL scale factors were NOT found in the topology file.
|       Using default value of 1.2.

| Note: 1-4 VDW scale factors were NOT found in the topology file.
|       Using default value of 2.0.
| Duplicated    0 dihedrals

| Duplicated    0 dihedrals

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

 getting new box info from bottom of inpcrd

 NATOM  =   22930 NTYPES =      17 NBONH =   21651 MBONA  =    1302
 NTHETH =    2789 MTHETA =    1772 NPHIH =    5026 MPHIA  =    3140
 NHPARM =       0 NPARM  =       0 NNB   =   41018 NRES   =    6980
 NBONA  =    1302 NTHETA =    1772 NPHIA =    3140 NUMBND =      45
 NUMANG =      91 NPTRA  =      33 NATYP =      32 NPHB   =       1
 IFBOX  =       1 NMXRS  =      25 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

| Coordinate Index Table dimensions:    15   13   12
| Direct force subcell size =     4.6709    4.6571    4.5436

     BOX TYPE: RECTILINEAR

--------------------------------------------------------------------------------
   2.  CONTROL  DATA  FOR  THE  RUN
--------------------------------------------------------------------------------

                                                                                

General flags:
     imin    =       0, nmropt  =       0

Nature and format of input:
     ntx     =       7, irest   =       1, ntrx    =       1

Nature and format of output:
     ntxo    =       1, ntpr    =       1, ntrx    =       1, ntwr    =   10000
     iwrap   =       0, ntwx    =       0, ntwv    =       0, ntwe    =       0
     ioutfm  =       0, ntwprt  =       0, idecomp =       0, rbornstat=      0

Potential function:
     ntf     =       2, ntb     =       1, igb     =       0, nsnb    =      25
     ipol    =       0, gbsa    =       0, iesp    =       0
     dielc   =   1.00000, cut     =   8.00000, intdiel =   1.00000

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

Molecular dynamics:
     nstlim  =        20, nscm    =      1000, nrespa  =         1
     t       =   0.00000, dt      =   0.00100, vlimit  =  20.00000

SHAKE:
     ntc     =       2, jfastw  =       0
     tol     =   0.00000

| Intermolecular bonds treatment:
|     no_intermolecular_bonds =       1

| Energy averages sample interval:
|     ene_avg_sampling =       1

Ewald parameters:
     verbose =       0, ew_type =       0, nbflag  =       1, use_pme =       1
     vdwmeth =       1, eedmeth =       1, netfrc  =       1
     Box X =   70.063   Box Y =   60.543   Box Z =   54.523
     Alpha =   90.000   Beta  =   90.000   Gamma =   90.000
     NFFT1 =   72       NFFT2 =   64       NFFT3 =   60
     Cutoff=    8.000   Tol   =0.100E-04
     Ewald Coefficient =  0.34864
     Interpolation order =    4

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

                                                                                
 begin time read from input coords =   510.050 ps

 
 Number of triangulated 3-point waters found:     6810

     Sum of charges from parm topology file =  -0.00000006
     Forcing neutrality...

| Dynamic Memory, Types Used:
| Reals              698255
| Integers           698786

| Nonbonded Pairs Initial Allocation:     3829883

--------------------------------------------------------------------------------
   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
 ---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
|  with   50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt.   2.47
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
|  with   50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt.   2.89
|---------------------------------------------------

 NSTEP =        1   TIME(PS) =     510.051  TEMP(K) =   301.29  PRESS =     0.0
 Etot   =    -57751.8144  EKtot   =     14110.5279  EPtot      =    -71862.3423
 BOND   =       452.1690  ANGLE   =      1277.0334  DIHED      =       968.3542
 1-4 NB =       545.9440  1-4 EEL =      6666.3920  VDWAALS    =      8109.3892
 EELEC  =    -89881.6242  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.3231E-04
 ------------------------------------------------------------------------------


 NSTEP =        2   TIME(PS) =     510.052  TEMP(K) =   301.16  PRESS =     0.0
 Etot   =    -57751.8172  EKtot   =     14104.5361  EPtot      =    -71856.3532
 BOND   =       454.7406  ANGLE   =      1280.2592  DIHED      =       969.1509
 1-4 NB =       547.4649  1-4 EEL =      6661.7833  VDWAALS    =      8112.2875
 EELEC  =    -89882.0395  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.2113E-04
 ------------------------------------------------------------------------------


 NSTEP =        3   TIME(PS) =     510.053  TEMP(K) =   300.92  PRESS =     0.0
 Etot   =    -57751.8458  EKtot   =     14093.2466  EPtot      =    -71845.0923
 BOND   =       459.7257  ANGLE   =      1284.1223  DIHED      =       971.1727
 1-4 NB =       549.0250  1-4 EEL =      6656.3558  VDWAALS    =      8116.0426
 EELEC  =    -89881.5364  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.3093E-04
 ------------------------------------------------------------------------------


 NSTEP =        4   TIME(PS) =     510.054  TEMP(K) =   300.56  PRESS =     0.0
 Etot   =    -57751.9322  EKtot   =     14076.6171  EPtot      =    -71828.5493
 BOND   =       466.5030  ANGLE   =      1288.5461  DIHED      =       974.2466
 1-4 NB =       550.4298  1-4 EEL =      6650.2845  VDWAALS    =      8120.4455
 EELEC  =    -89879.0048  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.5802E-04
 ------------------------------------------------------------------------------


 NSTEP =        5   TIME(PS) =     510.055  TEMP(K) =   300.11  PRESS =     0.0
 Etot   =    -57751.8238  EKtot   =     14055.5431  EPtot      =    -71807.3668
 BOND   =       474.1741  ANGLE   =      1293.2730  DIHED      =       978.0262
 1-4 NB =       551.4584  1-4 EEL =      6643.7780  VDWAALS    =      8125.2689
 EELEC  =    -89873.3454  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.4721E-04
 ------------------------------------------------------------------------------


 NSTEP =        6   TIME(PS) =     510.056  TEMP(K) =   299.61  PRESS =     0.0
 Etot   =    -57751.6541  EKtot   =     14031.8307  EPtot      =    -71783.4849
 BOND   =       481.6902  ANGLE   =      1297.7743  DIHED      =       982.0527
 1-4 NB =       551.9190  1-4 EEL =      6637.0660  VDWAALS    =      8130.5916
 EELEC  =    -89864.5786  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.6757E-04
 ------------------------------------------------------------------------------


 NSTEP =        7   TIME(PS) =     510.057  TEMP(K) =   299.10  PRESS =     0.0
 Etot   =    -57751.4692  EKtot   =     14007.9494  EPtot      =    -71759.4186
 BOND   =       488.0154  ANGLE   =      1301.2367  DIHED      =       985.8347
 1-4 NB =       551.7040  1-4 EEL =      6630.3791  VDWAALS    =      8136.0515
 EELEC  =    -89852.6399  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.7841E-04
 ------------------------------------------------------------------------------


 NSTEP =        8   TIME(PS) =     510.058  TEMP(K) =   298.64  PRESS =     0.0
 Etot   =    -57751.4377  EKtot   =     13986.5733  EPtot      =    -71738.0111
 BOND   =       492.3144  ANGLE   =      1302.7119  DIHED      =       988.9237
 1-4 NB =       550.8103  1-4 EEL =      6623.9284  VDWAALS    =      8141.6820
 EELEC  =    -89838.3817  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.1148E-03
 ------------------------------------------------------------------------------


 NSTEP =        9   TIME(PS) =     510.059  TEMP(K) =   298.29  PRESS =     0.0
 Etot   =    -57751.4687  EKtot   =     13969.9704  EPtot      =    -71721.4391
 BOND   =       494.1352  ANGLE   =      1301.4406  DIHED      =       990.9727
 1-4 NB =       549.3279  1-4 EEL =      6617.8892  VDWAALS    =      8147.4573
 EELEC  =    -89822.6621  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.1363E-03
 ------------------------------------------------------------------------------


 NSTEP =       10   TIME(PS) =     510.060  TEMP(K) =   298.06  PRESS =     0.0
 Etot   =    -57751.5457  EKtot   =     13959.3933  EPtot      =    -71710.9390
 BOND   =       493.5409  ANGLE   =      1297.2411  DIHED      =       991.7769
 1-4 NB =       547.4171  1-4 EEL =      6612.3958  VDWAALS    =      8153.5158
 EELEC  =    -89806.8266  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.1395E-03
 ------------------------------------------------------------------------------


 NSTEP =       11   TIME(PS) =     510.061  TEMP(K) =   297.96  PRESS =     0.0
 Etot   =    -57751.6765  EKtot   =     13954.7138  EPtot      =    -71706.3903
 BOND   =       491.1306  ANGLE   =      1290.7681  DIHED      =       991.3002
 1-4 NB =       545.2822  1-4 EEL =      6607.5450  VDWAALS    =      8160.0074
 EELEC  =    -89792.4237  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.1356E-03
 ------------------------------------------------------------------------------


 NSTEP =       12   TIME(PS) =     510.062  TEMP(K) =   297.96  PRESS =     0.0
 Etot   =    -57751.9280  EKtot   =     13954.4857  EPtot      =    -71706.4137
 BOND   =       487.9040  ANGLE   =      1283.4713  DIHED      =       989.6788
 1-4 NB =       543.1406  1-4 EEL =      6603.4075  VDWAALS    =      8166.9816
 EELEC  =    -89780.9975  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.1420E-03
 ------------------------------------------------------------------------------


 NSTEP =       13   TIME(PS) =     510.063  TEMP(K) =   298.00  PRESS =     0.0
 Etot   =    -57752.0165  EKtot   =     13956.5073  EPtot      =    -71708.5238
 BOND   =       484.9715  ANGLE   =      1277.2170  DIHED      =       987.1954
 1-4 NB =       541.1827  1-4 EEL =      6600.0426  VDWAALS    =      8174.5348
 EELEC  =    -89773.6677  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.1312E-03
 ------------------------------------------------------------------------------


 NSTEP =       14   TIME(PS) =     510.064  TEMP(K) =   298.05  PRESS =     0.0
 Etot   =    -57751.9433  EKtot   =     13958.6873  EPtot      =    -71710.6306
 BOND   =       483.1834  ANGLE   =      1273.6992  DIHED      =       984.2295
 1-4 NB =       539.5328  1-4 EEL =      6597.5101  VDWAALS    =      8182.6368
 EELEC  =    -89771.4223  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.1069E-03
 ------------------------------------------------------------------------------


 NSTEP =       15   TIME(PS) =     510.065  TEMP(K) =   298.07  PRESS =     0.0
 Etot   =    -57751.8757  EKtot   =     13959.8598  EPtot      =    -71711.7355
 BOND   =       482.8154  ANGLE   =      1273.8740  DIHED      =       981.2027
 1-4 NB =       538.2293  1-4 EEL =      6595.8748  VDWAALS    =      8191.2742
 EELEC  =    -89775.0059  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.1019E-03
 ------------------------------------------------------------------------------


 NSTEP =       16   TIME(PS) =     510.066  TEMP(K) =   298.08  PRESS =     0.0
 Etot   =    -57751.7345  EKtot   =     13960.1845  EPtot      =    -71711.9191
 BOND   =       483.4601  ANGLE   =      1277.6514  DIHED      =       978.5324
 1-4 NB =       537.2351  1-4 EEL =      6595.1998  VDWAALS    =      8200.3602
 EELEC  =    -89784.3581  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.8973E-04
 ------------------------------------------------------------------------------


 NSTEP =       17   TIME(PS) =     510.067  TEMP(K) =   298.09  PRESS =     0.0
 Etot   =    -57751.6639  EKtot   =     13960.9166  EPtot      =    -71712.5805
 BOND   =       484.2038  ANGLE   =      1283.9786  DIHED      =       976.5876
 1-4 NB =       536.4720  1-4 EEL =      6595.5301  VDWAALS    =      8209.7526
 EELEC  =    -89799.1052  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.8263E-04
 ------------------------------------------------------------------------------


 NSTEP =       18   TIME(PS) =     510.068  TEMP(K) =   298.15  PRESS =     0.0
 Etot   =    -57751.7250  EKtot   =     13963.6665  EPtot      =    -71715.3914
 BOND   =       484.0457  ANGLE   =      1291.2696  DIHED      =       975.6400
 1-4 NB =       535.8588  1-4 EEL =      6596.8725  VDWAALS    =      8219.2259
 EELEC  =    -89818.3040  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.8328E-04
 ------------------------------------------------------------------------------


 NSTEP =       19   TIME(PS) =     510.069  TEMP(K) =   298.28  PRESS =     0.0
 Etot   =    -57751.7544  EKtot   =     13969.5163  EPtot      =    -71721.2707
 BOND   =       482.3871  ANGLE   =      1297.9749  DIHED      =       975.8145
 1-4 NB =       535.3299  1-4 EEL =      6599.1784  VDWAALS    =      8228.6736
 EELEC  =    -89840.6291  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.1039E-03
 ------------------------------------------------------------------------------


 NSTEP =       20   TIME(PS) =     510.070  TEMP(K) =   298.47  PRESS =     0.0
 Etot   =    -57751.7266  EKtot   =     13978.4173  EPtot      =    -71730.1439
 BOND   =       479.3669  ANGLE   =      1303.0252  DIHED      =       977.0605
 1-4 NB =       534.8304  1-4 EEL =      6602.3385  VDWAALS    =      8237.3235
 EELEC  =    -89864.0889  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.8686E-04
 ------------------------------------------------------------------------------


      A V E R A G E S   O V E R      20 S T E P S


 NSTEP =       20   TIME(PS) =     510.070  TEMP(K) =   298.94  PRESS =     0.0
 Etot   =    -57751.7427  EKtot   =     14000.6571  EPtot      =    -71752.3998
 BOND   =       480.0239  ANGLE   =      1288.8284  DIHED      =       980.8876
 1-4 NB =       544.1297  1-4 EEL =      6619.6876  VDWAALS    =      8163.1751
 EELEC  =    -89829.1321  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 Ewald error estimate:   0.8952E-04
 ------------------------------------------------------------------------------


      R M S  F L U C T U A T I O N S


 NSTEP =       20   TIME(PS) =     510.070  TEMP(K) =     1.17  PRESS =     0.0
 Etot   =         0.1631  EKtot   =        54.6594  EPtot      =        54.6896
 BOND   =        12.0891  ANGLE   =         9.9261  DIHED      =         7.3516
 1-4 NB =         6.0734  1-4 EEL =        24.0705  VDWAALS    =        39.6044
 EELEC  =        40.3457  EHBOND  =         0.0000  RESTRAINT  =         0.0000
|E(PBS) =         0.1870
 Ewald error estimate:   0.3707E-04
 ------------------------------------------------------------------------------

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

|  NonSetup CPU Time in Major Routines:
|
|     Routine           Sec        %
|     ------------------------------
|     Nonbond           2.61   90.77
|     Bond              0.00    0.03
|     Angle             0.01    0.42
|     Dihedral          0.05    1.71
|     Shake             0.03    0.94
|     RunMD             0.18    6.13
|     Other             0.00    0.00
|     ------------------------------
|     Total             2.87

|  PME Nonbond Pairlist CPU Time:
|
|     Routine              Sec        %
|     ---------------------------------
|     Set Up Cit           0.00    0.10
|     Build List           0.27    9.40
|     ---------------------------------
|     Total                0.27    9.51

|  PME Direct Force CPU Time:
|
|     Routine              Sec        %
|     ---------------------------------
|     NonBonded Calc       1.80   62.71
|     Exclude Masked       0.04    1.29
|     Other                0.01    0.49
|     ---------------------------------
|     Total                1.85   64.48

|  PME Reciprocal Force CPU Time:
|
|     Routine              Sec        %
|     ---------------------------------
|     1D bspline           0.04    1.46
|     Grid Charges         0.05    1.71
|     Scalar Sum           0.08    2.92
|     Gradient Sum         0.08    2.65
|     FFT                  0.23    8.04
|     ---------------------------------
|     Total                0.48   16.78

|  Final Performance Info:
|     -----------------------------------------------------
|     Average timings for last      19 steps:
|         Elapsed(s) =       2.72 Per Step(ms) =     143.07
|             ns/day =       0.60   seconds/ns =  143065.69
|
|     Average timings for all steps:
|         Elapsed(s) =       2.95 Per Step(ms) =     147.63
|             ns/day =       0.59   seconds/ns =  147629.15
|     -----------------------------------------------------

|  Setup CPU time:            0.22 seconds
|  NonSetup CPU time:         2.87 seconds
|  Total CPU time:            3.09 seconds     0.00 hours

|  Setup wall time:           1    seconds
|  NonSetup wall time:        3    seconds
|  Total wall time:           4    seconds     0.00 hours