
          -------------------------------------------------------
          Amber 14 SANDER                              2014
          -------------------------------------------------------

| PMEMD implementation of SANDER, Release 14

| Run on 03/13/2014 at 12:08:25

|   Executable path: /work/00301/tg455746/GIT/amber-cuda5.0/bin/pmemd.cuda_SPFP.MPI
| Working directory: /work/00301/tg455746/GIT/amber-cuda5.0/test/cuda/scaledMD
|          Hostname: c557-003

  [-O]verwriting output

File Assignments:
|   MDIN: mdin                                                                  
|  MDOUT: mdout                                                                 
| INPCRD: dip.crd                                                               
|   PARM: dip.top                                                               
| RESTRT: restrt                                                                
|   REFC: refc                                                                  
|  MDVEL: mdvel                                                                 
|   MDEN: mden                                                                  
|  MDCRD: mdcrd                                                                 
| MDINFO: mdinfo                                                                
|LOGFILE: logfile                                                               
|  MDFRC: mdfrc                                                                 


 Here is the input file:

 short md, nve ensemble test SMD=1 PME                                         
 &cntrl                                                                        
  imin=0,irest=1,ntx=5,                                                        
  nstlim=25,dt=0.002,                                                          
  ntc=2,ntf=2,tol=0.000001,                                                    
  temp0=300.0,iwrap=1,                                                         
  cut=8.0, ntb=1,                                                              
  ntpr=2, ntwx=0,ntwr=0,                                                       
  ntt=0,ioutfm=0,ig=2221,ntave=0,                                              
  scaledmd=1,                                                                  
  scaledmd_lambda=0.70,                                                        
 /                                                                             
 &ewald                                                                        
  dsum_tol=0.000001,nfft1=96,                                                  
  nfft2=96,nfft3=96,netfrc=0                                                   
 /                                                                             


| Using Scaled MD to enhance sampling
| scaledMD scaling factor to potential energy: scaledMD_lambda =         0.700000000000
 
|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
|                     Version 14.0
| 
|                      01/31/2014
| 
| Implementation by:
|                    Ross C. Walker     (SDSC)
|                    Scott Le Grand     (nVIDIA)
| 
| CAUTION: The CUDA code is currently experimental.
|          You use it at your own risk. Be sure to
|          check ALL results carefully.
| 
| Precision model in use:
|      [SPFP] - Mixed Single/Double/Fixed Point Precision.
|               (Default)
| 
|--------------------------------------------------------
 
|----------------- CITATION INFORMATION -----------------
|
|    When publishing work that utilized the CUDA version
|    of AMBER, please cite the following in addition to
|    the regular AMBER citations:
|
|  - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan
|    Poole; Scott Le Grand; Ross C. Walker "Routine
|    microsecond molecular dynamics simulations with
|    AMBER - Part II: Particle Mesh Ewald", J. Chem.
|    Theory Comput., 2013, 9 (9), pp3878-3888,
|    DOI: 10.1021/ct400314y.
|
|  - Andreas W. Goetz; Mark J. Williamson; Dong Xu;
|    Duncan Poole; Scott Le Grand; Ross C. Walker
|    "Routine microsecond molecular dynamics simulations
|    with AMBER - Part I: Generalized Born", J. Chem.
|    Theory Comput., 2012, 8 (5), pp1542-1555.
|
|  - Scott Le Grand; Andreas W. Goetz; Ross C. Walker
|    "SPFP: Speed without compromise - a mixed precision
|    model for GPU accelerated molecular dynamics
|    simulations.", Comp. Phys. Comm., 2013, 184
|    pp374-380, DOI: 10.1016/j.cpc.2012.09.022
|
|--------------------------------------------------------
 
|------------------- GPU DEVICE INFO --------------------
|
|                         Task ID:      0
|            CUDA_VISIBLE_DEVICES: not set
|   CUDA Capable Devices Detected:      1
|           CUDA Device ID in use:      0
|                CUDA Device Name: Tesla K20m
|     CUDA Device Global Mem Size:   4799 MB
| CUDA Device Num Multiprocessors:     13
|           CUDA Device Core Freq:   0.71 GHz
|
|
|                         Task ID:      1
|            CUDA_VISIBLE_DEVICES: not set
|   CUDA Capable Devices Detected:      1
|           CUDA Device ID in use:      0
|                CUDA Device Name: Tesla K20m
|     CUDA Device Global Mem Size:   4799 MB
| CUDA Device Num Multiprocessors:     13
|           CUDA Device Core Freq:   0.71 GHz
|
|--------------------------------------------------------
 
|---------------- GPU PEER TO PEER INFO -----------------
|
|   Peer to Peer support: DISABLED
|
|              (MPI tasks span multiple nodes)
|
|--------------------------------------------------------
 
 
| Conditional Compilation Defines Used:
| MPI
| PUBFFT
| BINTRAJ
| CUDA

| Largest sphere to fit in unit cell has radius =    12.473

| New format PARM file being parsed.
| Version =    1.000 Date = 09/27/06 Time = 14:19:31

| 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  =    1912 NTYPES =       9 NBONH =    1902 MBONA  =       9
 NTHETH =      25 MTHETA =      11 NPHIH =      41 MPHIA  =      17
 NHPARM =       0 NPARM  =       0 NNB   =    2619 NRES   =     633
 NBONA  =       9 NTHETA =      11 NPHIA =      17 NUMBND =      10
 NUMANG =      16 NPTRA  =      16 NATYP =       9 NPHB   =       1
 IFBOX  =       1 NMXRS  =      10 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

| Coordinate Index Table dimensions:     5    5    4
| Direct force subcell size =     5.3514    5.8120    6.2366

     BOX TYPE: RECTILINEAR

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

ACE                                                                             

General flags:
     imin    =       0, nmropt  =       0

Nature and format of input:
     ntx     =       5, irest   =       1, ntrx    =       1

Nature and format of output:
     ntxo    =       1, ntpr    =       2, ntrx    =       1, ntwr    =       0
     iwrap   =       1, 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  =        25, nscm    =      1000, nrespa  =         1
     t       =   0.00000, dt      =   0.00200, vlimit  =  -1.00000

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

| Intermolecular bonds treatment:
|     no_intermolecular_bonds =       1

| Energy averages sample interval:
|     ene_avg_sampling =       2

Ewald parameters:
     verbose =       0, ew_type =       0, nbflag  =       1, use_pme =       1
     vdwmeth =       1, eedmeth =       1, netfrc  =       0
     Box X =   26.757   Box Y =   29.060   Box Z =   24.946
     Alpha =   90.000   Beta  =   90.000   Gamma =   90.000
     NFFT1 =   96       NFFT2 =   96       NFFT3 =   96
     Cutoff=    8.000   Tol   =0.100E-05
     Ewald Coefficient =  0.39467
     Interpolation order =    4

| PMEMD ewald parallel performance parameters:
|     block_fft =    0
|     fft_blk_y_divisor =    2
|     excl_recip =    0
|     excl_master =    0
|     atm_redist_freq =  320

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

ACE                                                                             
 begin time read from input coords =    40.000 ps

 
 Number of triangulated 3-point waters found:      630

     Sum of charges from parm topology file =  -0.00000000
     Forcing neutrality...

| Dynamic Memory, Types Used:
| Reals              645289
| Integers           163014

| Nonbonded Pairs Initial Allocation:      217968

| GPU memory information (estimate):
| KB of GPU memory in use:     16768
| KB of CPU memory in use:     16768

| Running AMBER/MPI version on    2 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 =   0.8987E-11   at   2.875760
 ---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
|  with   50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt.   2.52
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
|  with   50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt.   2.92
|---------------------------------------------------

 NSTEP =        2   TIME(PS) =      40.004  TEMP(K) =   309.78  PRESS =     0.0
 Etot   =     -3081.4516  EKtot   =      1179.1511  EPtot      =     -4260.6027
 BOND   =         2.5363  ANGLE   =        12.5132  DIHED      =        10.0646
 1-4 NB =         3.7351  1-4 EEL =        50.6372  VDWAALS    =       877.8282
 EELEC  =     -7043.8899  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =        4   TIME(PS) =      40.008  TEMP(K) =   296.20  PRESS =     0.0
 Etot   =     -3080.8223  EKtot   =      1127.4718  EPtot      =     -4208.2941
 BOND   =         7.4743  ANGLE   =        13.1204  DIHED      =        10.2267
 1-4 NB =         4.0242  1-4 EEL =        51.0858  VDWAALS    =       887.0979
 EELEC  =     -6984.8780  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =        6   TIME(PS) =      40.012  TEMP(K) =   278.44  PRESS =     0.0
 Etot   =     -3080.3283  EKtot   =      1059.8748  EPtot      =     -4140.2030
 BOND   =         6.8082  ANGLE   =        11.0936  DIHED      =        10.0216
 1-4 NB =         4.5764  1-4 EEL =        49.6852  VDWAALS    =       902.0264
 EELEC  =     -6898.7872  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =        8   TIME(PS) =      40.016  TEMP(K) =   263.67  PRESS =     0.0
 Etot   =     -3080.0510  EKtot   =      1003.6494  EPtot      =     -4083.7004
 BOND   =         3.1688  ANGLE   =        11.6662  DIHED      =         9.6993
 1-4 NB =         5.1350  1-4 EEL =        48.1470  VDWAALS    =       921.0111
 EELEC  =     -6832.6850  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =       10   TIME(PS) =      40.020  TEMP(K) =   255.74  PRESS =     0.0
 Etot   =     -3079.9935  EKtot   =       973.4834  EPtot      =     -4053.4769
 BOND   =         3.3777  ANGLE   =        14.1871  DIHED      =         9.5501
 1-4 NB =         5.5356  1-4 EEL =        47.3149  VDWAALS    =       941.5380
 EELEC  =     -6812.1848  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =       12   TIME(PS) =      40.024  TEMP(K) =   254.97  PRESS =     0.0
 Etot   =     -3080.2397  EKtot   =       970.5323  EPtot      =     -4050.7720
 BOND   =         6.2367  ANGLE   =        13.6970  DIHED      =         9.2886
 1-4 NB =         5.4640  1-4 EEL =        46.8372  VDWAALS    =       960.8307
 EELEC  =     -6829.1713  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =       14   TIME(PS) =      40.028  TEMP(K) =   257.69  PRESS =     0.0
 Etot   =     -3080.6380  EKtot   =       980.8884  EPtot      =     -4061.5264
 BOND   =         9.8331  ANGLE   =         7.3429  DIHED      =         8.9194
 1-4 NB =         5.0996  1-4 EEL =        46.1894  VDWAALS    =       976.4918
 EELEC  =     -6856.0567  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =       16   TIME(PS) =      40.032  TEMP(K) =   258.41  PRESS =     0.0
 Etot   =     -3080.6277  EKtot   =       983.6167  EPtot      =     -4064.2444
 BOND   =        11.9927  ANGLE   =         8.3853  DIHED      =         9.1398
 1-4 NB =         4.6595  1-4 EEL =        45.4967  VDWAALS    =       986.6548
 EELEC  =     -6872.3923  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =       18   TIME(PS) =      40.036  TEMP(K) =   257.46  PRESS =     0.0
 Etot   =     -3080.2884  EKtot   =       979.9956  EPtot      =     -4060.2840
 BOND   =         8.2128  ANGLE   =        16.1592  DIHED      =         9.7588
 1-4 NB =         4.4710  1-4 EEL =        45.5830  VDWAALS    =       991.6937
 EELEC  =     -6876.2841  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =       20   TIME(PS) =      40.040  TEMP(K) =   259.00  PRESS =     0.0
 Etot   =     -3080.5513  EKtot   =       985.8682  EPtot      =     -4066.4195
 BOND   =         2.2052  ANGLE   =        10.8424  DIHED      =        10.0317
 1-4 NB =         4.4845  1-4 EEL =        46.9673  VDWAALS    =       992.8056
 EELEC  =     -6876.5075  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =       22   TIME(PS) =      40.044  TEMP(K) =   260.05  PRESS =     0.0
 Etot   =     -3080.5137  EKtot   =       989.8636  EPtot      =     -4070.3773
 BOND   =         4.7957  ANGLE   =         6.6750  DIHED      =         9.7626
 1-4 NB =         4.5348  1-4 EEL =        48.9883  VDWAALS    =       990.8360
 EELEC  =     -6880.4171  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =       24   TIME(PS) =      40.048  TEMP(K) =   260.62  PRESS =     0.0
 Etot   =     -3080.2435  EKtot   =       992.0588  EPtot      =     -4072.3023
 BOND   =         7.8258  ANGLE   =        12.3251  DIHED      =         9.2101
 1-4 NB =         4.5511  1-4 EEL =        50.4267  VDWAALS    =       985.6649
 EELEC  =     -6887.5783  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


      A V E R A G E S   O V E R      12 S T E P S


 NSTEP =       25   TIME(PS) =      40.050  TEMP(K) =   267.67  PRESS =     0.0
 Etot   =     -3080.4791  EKtot   =      1018.8712  EPtot      =     -4099.3503
 BOND   =         6.2056  ANGLE   =        11.5006  DIHED      =         9.6394
 1-4 NB =         4.6892  1-4 EEL =        48.1132  VDWAALS    =       951.2066
 EELEC  =     -6887.5693  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


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


 NSTEP =       25   TIME(PS) =      40.050  TEMP(K) =    17.07  PRESS =     0.0
 Etot   =         0.3773  EKtot   =        64.9614  EPtot      =        65.2520
 BOND   =         2.9432  ANGLE   =         2.7230  DIHED      =         0.4023
 1-4 NB =         0.5150  1-4 EEL =         1.9219  VDWAALS    =        41.8672
 EELEC  =        63.0216  EHBOND  =         0.0000  RESTRAINT  =         0.0000
|E(PBS) =         0.2110
 ------------------------------------------------------------------------------

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

|  NonSetup CPU Time in Major Routines, Average for All Tasks:
|
|     Routine           Sec        %
|     ------------------------------
|     DataDistrib       0.00    1.57
|     Nonbond           0.05   83.46
|     Bond              0.00    0.00
|     Angle             0.00    0.00
|     Dihedral          0.00    0.00
|     Shake             0.00    0.00
|     RunMD             0.01   14.17
|     Other             0.00    0.79
|     ------------------------------
|     Total             0.06

|  PME Nonbond Pairlist CPU Time, Average for All Tasks:
|
|     Routine              Sec        %
|     ---------------------------------
|     Set Up Cit           0.00    0.00
|     Build List           0.00    0.00
|     ---------------------------------
|     Total                0.00    0.00

|  PME Direct Force CPU Time, Average for All Tasks:
|
|     Routine              Sec        %
|     ---------------------------------
|     NonBonded Calc       0.00    0.00
|     Exclude Masked       0.00    0.00
|     Other                0.00    0.79
|     ---------------------------------
|     Total                0.00    0.79

|  PME Reciprocal Force CPU Time, Average for All Tasks:
|
|     Routine              Sec        %
|     ---------------------------------
|     1D bspline           0.00    0.00
|     Grid Charges         0.00    0.00
|     Scalar Sum           0.00    0.00
|     Gradient Sum         0.00    0.00
|     FFT                  0.00    0.00
|     ---------------------------------
|     Total                0.00    0.00

|  PME Load Balancing CPU Time, Average for All Tasks:
|
|     Routine                 Sec        %
|     ------------------------------------
|     Atom Reassign           0.00    0.00
|     Image Reassign          0.00    0.00
|     FFT Reassign            0.00    0.00
|     ------------------------------------
|     Total                   0.00    0.00

|  Final Performance Info:
|     -----------------------------------------------------
|     Average timings for last      23 steps:
|         Elapsed(s) =       0.06 Per Step(ms) =       2.63
|             ns/day =      65.58   seconds/ns =    1317.50
|
|     Average timings for all steps:
|         Elapsed(s) =       0.11 Per Step(ms) =       4.30
|             ns/day =      40.17   seconds/ns =    2150.74
|     -----------------------------------------------------

|  Master Setup CPU time:            1.79 seconds
|  Master NonSetup CPU time:         0.05 seconds
|  Master Total CPU time:            1.84 seconds     0.00 hours

|  Master Setup wall time:           2    seconds
|  Master NonSetup wall time:        1    seconds
|  Master Total wall time:           3    seconds     0.00 hours
