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

| PMEMD implementation of SANDER, Release 14

| Run on 03/13/2014 at 12:09:51

|   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/lipid_npt_tests
|          Hostname: c557-003

  [-O]verwriting output

File Assignments:
|   MDIN: mdin                                                                  
|  MDOUT: mdout_nvt_lipid14                                                     
| INPCRD: inpcrd                                                                
|   PARM: prmtop                                                                
| 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                                                        
 &cntrl                                                                        
   imin=0, ntx=5, irest=1,                                                     
   ntc=2, ntf=2, tol=0.0000001,                                                
   nstlim=20, ntt=1, tautp=5.0,                                                
   temp0=303.0,                                                                
   ntb=1, ntp=0, cut=10.0,                                                     
   ntpr=1, ntwr=10000,ntwx=0,                                                  
   dt=0.002,                                                                   
 /                                                                             
 &ewald                                                                        
  netfrc=0, NFFT1=64, NFFT2=72, NFFT3=80,                                      
 /                                                                             


 
|--------------------- 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 =    30.733

| New format PARM file being parsed.
| Version =    1.000 Date = 10/11/13 Time = 15:52:38

| Note: 1-4 EEL scale factors are being read from the topology file.

| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated    0 dihedrals

| Duplicated    0 dihedrals

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

 getting new box info from bottom of inpcrd

 NATOM  =   30282 NTYPES =      15 NBONH =   23346 MBONA  =    6784
 NTHETH =   25728 MTHETA =    7808 NPHIH =   41984 MPHIA  =   25088
 NHPARM =       0 NPARM  =       0 NNB   =  114864 NRES   =    4606
 NBONA  =    6784 NTHETA =    7808 NPHIA =   25088 NUMBND =      18
 NUMANG =      30 NPTRA  =      54 NATYP =      18 NPHB   =       1
 IFBOX  =       1 NMXRS  =      50 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

| Coordinate Index Table dimensions:    10   10   12
| Direct force subcell size =     6.1466    6.5010    6.0162

     BOX TYPE: RECTILINEAR

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

default_name                                                                    

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    =       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     =  10.00000, intdiel =   1.00000

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

Molecular dynamics:
     nstlim  =        20, nscm    =      1000, nrespa  =         1
     t       =   0.00000, dt      =   0.00200, vlimit  =  -1.00000

Berendsen (weak-coupling) temperature regulation:
     temp0   = 303.00000, tempi   =   0.00000, tautp   =   5.00000

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  =       0
     Box X =   61.466   Box Y =   65.010   Box Z =   72.195
     Alpha =   90.000   Beta  =   90.000   Gamma =   90.000
     NFFT1 =   64       NFFT2 =   72       NFFT3 =   80
     Cutoff=   10.000   Tol   =0.100E-04
     Ewald Coefficient =  0.27511
     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
--------------------------------------------------------------------------------

default_name                                                                    
 begin time read from input coords =919999.993 ps

 
 Number of triangulated 3-point waters found:     4198

     Sum of charges from parm topology file =  -0.00102514
     Forcing neutrality...

| Dynamic Memory, Types Used:
| Reals             1283872
| Integers          3047410

| Nonbonded Pairs Initial Allocation:     5932243

| GPU memory information (estimate):
| KB of GPU memory in use:     62277
| KB of CPU memory in use:     46328

| 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 =   0.8314E-11   at   2.736960
 ---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
|  with   50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt.   2.33
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
|  with   50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt.   2.80
|---------------------------------------------------

 NSTEP =        1   TIME(PS) =  919999.995  TEMP(K) =   300.13  PRESS =     0.0
 Etot   =    -32240.8859  EKtot   =     20128.4199  EPtot      =    -52369.3059
 BOND   =      2197.4430  ANGLE   =      9387.2922  DIHED      =      6275.5612
 1-4 NB =      1872.7797  1-4 EEL =     -2407.7819  VDWAALS    =     -1264.7425
 EELEC  =    -68429.8576  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =        2   TIME(PS) =  919999.997  TEMP(K) =   301.57  PRESS =     0.0
 Etot   =    -32246.0923  EKtot   =     20224.8203  EPtot      =    -52470.9126
 BOND   =      2172.2302  ANGLE   =      9312.9638  DIHED      =      6272.3039
 1-4 NB =      1873.5221  1-4 EEL =     -2407.9263  VDWAALS    =     -1241.2221
 EELEC  =    -68452.7843  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =        3   TIME(PS) =  919999.999  TEMP(K) =   302.76  PRESS =     0.0
 Etot   =    -32248.8375  EKtot   =     20304.6641  EPtot      =    -52553.5015
 BOND   =      2184.7615  ANGLE   =      9231.6815  DIHED      =      6269.2435
 1-4 NB =      1873.7839  1-4 EEL =     -2409.2646  VDWAALS    =     -1231.4555
 EELEC  =    -68472.2519  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =        4   TIME(PS) =  920000.001  TEMP(K) =   303.10  PRESS =     0.0
 Etot   =    -32248.3872  EKtot   =     20327.3730  EPtot      =    -52575.7603
 BOND   =      2224.6228  ANGLE   =      9193.8653  DIHED      =      6264.0500
 1-4 NB =      1873.5433  1-4 EEL =     -2411.4454  VDWAALS    =     -1233.2443
 EELEC  =    -68487.1520  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =        5   TIME(PS) =  920000.003  TEMP(K) =   302.70  PRESS =     0.0
 Etot   =    -32245.5587  EKtot   =     20300.3633  EPtot      =    -52545.9220
 BOND   =      2264.2247  ANGLE   =      9210.6911  DIHED      =      6257.0067
 1-4 NB =      1873.4035  1-4 EEL =     -2413.6220  VDWAALS    =     -1239.7590
 EELEC  =    -68497.8670  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =        6   TIME(PS) =  920000.005  TEMP(K) =   302.17  PRESS =     0.0
 Etot   =    -32242.5349  EKtot   =     20264.9844  EPtot      =    -52507.5192
 BOND   =      2284.2584  ANGLE   =      9250.3272  DIHED      =      6251.1222
 1-4 NB =      1874.2356  1-4 EEL =     -2414.8816  VDWAALS    =     -1246.4300
 EELEC  =    -68506.1510  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =        7   TIME(PS) =  920000.007  TEMP(K) =   302.16  PRESS =     0.0
 Etot   =    -32242.0371  EKtot   =     20264.0957  EPtot      =    -52506.1328
 BOND   =      2279.7632  ANGLE   =      9270.0325  DIHED      =      6250.3239
 1-4 NB =      1876.0861  1-4 EEL =     -2414.9317  VDWAALS    =     -1253.9486
 EELEC  =    -68513.4582  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =        8   TIME(PS) =  920000.009  TEMP(K) =   302.74  PRESS =     0.0
 Etot   =    -32244.9675  EKtot   =     20303.1465  EPtot      =    -52548.1139
 BOND   =      2255.3944  ANGLE   =      9260.5995  DIHED      =      6256.8510
 1-4 NB =      1878.0785  1-4 EEL =     -2414.3501  VDWAALS    =     -1263.7718
 EELEC  =    -68520.9155  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =        9   TIME(PS) =  920000.011  TEMP(K) =   303.32  PRESS =     0.0
 Etot   =    -32247.7216  EKtot   =     20341.9863  EPtot      =    -52589.7079
 BOND   =      2222.3030  ANGLE   =      9256.9201  DIHED      =      6269.8911
 1-4 NB =      1879.1265  1-4 EEL =     -2414.1149  VDWAALS    =     -1274.6050
 EELEC  =    -68529.2288  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =       10   TIME(PS) =  920000.013  TEMP(K) =   303.29  PRESS =     0.0
 Etot   =    -32247.5205  EKtot   =     20340.2988  EPtot      =    -52587.8194
 BOND   =      2194.0612  ANGLE   =      9292.7861  DIHED      =      6287.0331
 1-4 NB =      1879.2477  1-4 EEL =     -2414.8950  VDWAALS    =     -1287.0215
 EELEC  =    -68539.0310  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =       11   TIME(PS) =  920000.015  TEMP(K) =   302.70  PRESS =     0.0
 Etot   =    -32244.7519  EKtot   =     20300.6953  EPtot      =    -52545.4472
 BOND   =      2179.5209  ANGLE   =      9354.0881  DIHED      =      6305.1226
 1-4 NB =      1880.0547  1-4 EEL =     -2416.7276  VDWAALS    =     -1298.6202
 EELEC  =    -68548.8857  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =       12   TIME(PS) =  920000.017  TEMP(K) =   302.14  PRESS =     0.0
 Etot   =    -32242.4266  EKtot   =     20262.7207  EPtot      =    -52505.1473
 BOND   =      2178.4018  ANGLE   =      9393.8403  DIHED      =      6318.8673
 1-4 NB =      1882.8513  1-4 EEL =     -2419.1783  VDWAALS    =     -1304.0083
 EELEC  =    -68555.9214  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =       13   TIME(PS) =  920000.019  TEMP(K) =   302.05  PRESS =     0.0
 Etot   =    -32243.8013  EKtot   =     20256.7871  EPtot      =    -52500.5884
 BOND   =      2185.2933  ANGLE   =      9388.1903  DIHED      =      6322.7365
 1-4 NB =      1886.5626  1-4 EEL =     -2421.6574  VDWAALS    =     -1304.2617
 EELEC  =    -68557.4519  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =       14   TIME(PS) =  920000.021  TEMP(K) =   302.18  PRESS =     0.0
 Etot   =    -32246.4470  EKtot   =     20265.3105  EPtot      =    -52511.7576
 BOND   =      2198.5241  ANGLE   =      9360.3877  DIHED      =      6316.6537
 1-4 NB =      1889.7527  1-4 EEL =     -2423.5896  VDWAALS    =     -1300.4136
 EELEC  =    -68553.0727  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =       15   TIME(PS) =  920000.023  TEMP(K) =   301.98  PRESS =     0.0
 Etot   =    -32246.1678  EKtot   =     20251.9648  EPtot      =    -52498.1326
 BOND   =      2220.6820  ANGLE   =      9345.4781  DIHED      =      6307.2334
 1-4 NB =      1891.4108  1-4 EEL =     -2424.4280  VDWAALS    =     -1292.9902
 EELEC  =    -68545.5187  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =       16   TIME(PS) =  920000.025  TEMP(K) =   301.51  PRESS =     0.0
 Etot   =    -32242.5752  EKtot   =     20220.6465  EPtot      =    -52463.2217
 BOND   =      2247.5855  ANGLE   =      9346.2769  DIHED      =      6301.7521
 1-4 NB =      1889.9537  1-4 EEL =     -2423.7297  VDWAALS    =     -1286.1673
 EELEC  =    -68538.8929  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =       17   TIME(PS) =  920000.027  TEMP(K) =   301.46  PRESS =     0.0
 Etot   =    -32240.4047  EKtot   =     20217.5996  EPtot      =    -52458.0043
 BOND   =      2263.9431  ANGLE   =      9333.6363  DIHED      =      6301.4134
 1-4 NB =      1886.1512  1-4 EEL =     -2421.3372  VDWAALS    =     -1285.2318
 EELEC  =    -68536.5795  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =       18   TIME(PS) =  920000.029  TEMP(K) =   302.23  PRESS =     0.0
 Etot   =    -32243.1514  EKtot   =     20269.2773  EPtot      =    -52512.4287
 BOND   =      2258.6662  ANGLE   =      9290.3632  DIHED      =      6301.4777
 1-4 NB =      1882.7470  1-4 EEL =     -2417.5336  VDWAALS    =     -1289.2323
 EELEC  =    -68538.9170  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =       19   TIME(PS) =  920000.031  TEMP(K) =   303.27  PRESS =     0.0
 Etot   =    -32248.1082  EKtot   =     20338.5508  EPtot      =    -52586.6590
 BOND   =      2240.0551  ANGLE   =      9244.7724  DIHED      =      6297.7509
 1-4 NB =      1880.9340  1-4 EEL =     -2413.0171  VDWAALS    =     -1294.4014
 EELEC  =    -68542.7528  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


 NSTEP =       20   TIME(PS) =  920000.033  TEMP(K) =   303.56  PRESS =     0.0
 Etot   =    -32249.5906  EKtot   =     20358.4707  EPtot      =    -52608.0613
 BOND   =      2226.4570  ANGLE   =      9247.4553  DIHED      =      6290.9241
 1-4 NB =      1879.9592  1-4 EEL =     -2408.7346  VDWAALS    =     -1299.7816
 EELEC  =    -68544.3408  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


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


 NSTEP =       20   TIME(PS) =  920000.033  TEMP(K) =   302.35  PRESS =     0.0
 Etot   =    -32245.0984  EKtot   =     20277.1088  EPtot      =    -52522.2072
 BOND   =      2223.9096  ANGLE   =      9298.5824  DIHED      =      6285.8659
 1-4 NB =      1880.2092  1-4 EEL =     -2415.6573  VDWAALS    =     -1274.5654
 EELEC  =    -68520.5515  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------


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


 NSTEP =       20   TIME(PS) =  920000.033  TEMP(K) =     0.80  PRESS =     0.0
 Etot   =         2.6998  EKtot   =        53.3848  EPtot      =        55.5137
 BOND   =        35.3566  ANGLE   =        60.3666  DIHED      =        22.9918
 1-4 NB =         5.8842  1-4 EEL =         5.1748  VDWAALS    =        24.8010
 EELEC  =        35.0295  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 ------------------------------------------------------------------------------

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

|  NonSetup CPU Time in Major Routines, Average for All Tasks:
|
|     Routine           Sec        %
|     ------------------------------
|     DataDistrib       0.00    0.29
|     Nonbond           0.06   35.65
|     Bond              0.00    0.00
|     Angle             0.00    0.00
|     Dihedral          0.00    0.00
|     Shake             0.00    0.00
|     RunMD             0.11   63.77
|     Other             0.00    0.29
|     ------------------------------
|     Total             0.17

|  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    0.00
|     ---------------------------------
|     Total                0.00    0.00

|  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      19 steps:
|         Elapsed(s) =       0.28 Per Step(ms) =      14.63
|             ns/day =      11.81   seconds/ns =    7317.07
|
|     Average timings for all steps:
|         Elapsed(s) =       0.29 Per Step(ms) =      14.41
|             ns/day =      11.99   seconds/ns =    7205.27
|     -----------------------------------------------------

|  Master Setup CPU time:            2.03 seconds
|  Master NonSetup CPU time:         0.28 seconds
|  Master Total CPU time:            2.31 seconds     0.00 hours

|  Master Setup wall time:           3    seconds
|  Master NonSetup wall time:        0    seconds
|  Master Total wall time:           3    seconds     0.00 hours
