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

| PMEMD implementation of SANDER, Release 12

| Run on 06/25/2016 at 18:34:08

  [-O]verwriting output

File Assignments:
|   MDIN: min_2.in                                                              
|  MDOUT: min_2.out                                                             
| INPCRD: min_1.rst                                                             
|   PARM: ./acetone.top                                                         
| RESTRT: min_2.rst                                                             
|   REFC: min_1.rst                                                             
|  MDVEL: mdvel                                                                 
|   MDEN: mden                                                                  
|  MDCRD: mdcrd                                                                 
| MDINFO: mdinfo                                                                


 Here is the input file:

energy minimization                                                            
 &cntrl                                                                        
   iwrap=1, ntxo=2, ioutfm=1,                                                  
   imin=1, maxcyc=1000, ntmin=1, ncyc=500,                                     
   ntwr = 5000, ntpr = 100,                                                    
 &end                                                                          
END                                                                            
END                                                                            
                                                                               
                                                                               
                                                                               
                                                                               


 
|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
|                    Version 12.3.1
| 
|                      08/07/2013
| 
| Implementation by:
|                    Ross C. Walker     (SDSC)
|                    Scott Le Grand     (nVIDIA)
|                    Duncan Poole       (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, 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 --------------------
|
|   CUDA Capable Devices Detected:      1
|           CUDA Device ID in use:      0
|                CUDA Device Name: GeForce GTX 670
|     CUDA Device Global Mem Size:   2046 MB
| CUDA Device Num Multiprocessors:      7
|           CUDA Device Core Freq:   0.98 GHz
|
|--------------------------------------------------------
 
 
| Conditional Compilation Defines Used:
| DIRFRC_COMTRANS
| DIRFRC_EFS
| DIRFRC_NOVEC
| PUBFFT
| FFTLOADBAL_2PROC
| BINTRAJ
| CUDA

| Largest sphere to fit in unit cell has radius =    18.105

| New format PARM file being parsed.
| Version =    1.000 Date = 06/25/16 Time = 18:09:31

| 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  =    3970 NTYPES =       4 NBONH =    2382 MBONA  =    1191
 NTHETH =    4764 MTHETA =    1191 NPHIH =    9525 MPHIA  =     397
 NHPARM =       0 NPARM  =       0 NNB   =   14689 NRES   =     397
 NBONA  =    1191 NTHETA =    1191 NPHIA =     397 NUMBND =       3
 NUMANG =       4 NPTRA  =       4 NATYP =       4 NPHB   =       0
 IFBOX  =       1 NMXRS  =      10 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

| Coordinate Index Table dimensions:     8   10   10
| Direct force subcell size =     4.5263    4.6226    4.7220

     BOX TYPE: RECTILINEAR

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

ACT                                                                             

General flags:
     imin    =       1, nmropt  =       0

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

Nature and format of output:
     ntxo    =       2, ntpr    =     100, ntrx    =       1, ntwr    =    5000
     iwrap   =       1, ntwx    =       0, ntwv    =       0, ntwe    =       0
     ioutfm  =       1, 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

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

Energy minimization:
     maxcyc  =    1000, ncyc    =     500, ntmin   =       1
     dx0     =   0.01000, drms    =   0.00010

| 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 =   36.210   Box Y =   46.226   Box Z =   47.220
     Alpha =   90.000   Beta  =   90.000   Gamma =   90.000
     NFFT1 =   40       NFFT2 =   48       NFFT3 =   48
     Cutoff=    8.000   Tol   =0.100E-04
     Ewald Coefficient =  0.34864
     Interpolation order =    4

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

ACT                                                                             
 begin time read from input coords =     0.000 ps

 
 Number of triangulated 3-point waters found:        0

     Sum of charges from parm topology file =   0.00000044
     Forcing neutrality...

| Dynamic Memory, Types Used:
| Reals              210254
| Integers           297345

| Nonbonded Pairs Initial Allocation:      663089

| GPU memory information (estimate):
| KB of GPU memory in use:     11160
| KB of CPU memory in use:      6960

--------------------------------------------------------------------------------
   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       ENERGY          RMS            GMAX         NAME    NUMBER
      1      -9.3787E+03     5.2152E-02     5.7340E-01     O3       1860

 BOND    =        0.7833  ANGLE   =       34.4501  DIHED      =     1899.7631
 VDWAALS =    -1136.0656  EEL     =      950.2486  HBOND      =        0.0000
 1-4 VDW =      194.0583  1-4 EEL =   -11321.9474  RESTRAINT  =        0.0000


   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    100      -9.3790E+03     5.1851E-02     3.0879E-01     C2       1945

 BOND    =        0.8169  ANGLE   =       33.8126  DIHED      =     1899.7870
 VDWAALS =    -1136.1387  EEL     =      950.0812  HBOND      =        0.0000
 1-4 VDW =      194.4164  1-4 EEL =   -11321.7455  RESTRAINT  =        0.0000


   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    200      -9.3792E+03     3.8770E-02     2.8077E-01     O3       2110

 BOND    =        0.7992  ANGLE   =       33.6419  DIHED      =     1899.8300
 VDWAALS =    -1136.1904  EEL     =      950.2146  HBOND      =        0.0000
 1-4 VDW =      194.4746  1-4 EEL =   -11321.9259  RESTRAINT  =        0.0000


   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    300      -9.3793E+03     1.9169E-02     2.4493E-01     O3       2140

 BOND    =        0.8068  ANGLE   =       33.7374  DIHED      =     1899.8088
 VDWAALS =    -1136.2670  EEL     =      949.9483  HBOND      =        0.0000
 1-4 VDW =      194.4451  1-4 EEL =   -11321.8225  RESTRAINT  =        0.0000


   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    400      -9.3795E+03     1.4525E-02     2.3083E-01     O3       2110

 BOND    =        0.8028  ANGLE   =       33.7021  DIHED      =     1899.8220
 VDWAALS =    -1136.3337  EEL     =      949.8889  HBOND      =        0.0000
 1-4 VDW =      194.4563  1-4 EEL =   -11321.8599  RESTRAINT  =        0.0000


   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    500      -9.3797E+03     6.1665E-02     3.8521E-01     C2       2025

 BOND    =        0.7982  ANGLE   =       33.5981  DIHED      =     1899.8529
 VDWAALS =    -1136.3935  EEL     =      949.9380  HBOND      =        0.0000
 1-4 VDW =      194.4893  1-4 EEL =   -11321.9722  RESTRAINT  =        0.0000


   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    600      -9.3905E+03     7.5778E-02     1.5947E+00     O3       2120

 BOND    =        0.8467  ANGLE   =       33.9340  DIHED      =     1900.2203
 VDWAALS =    -1139.8821  EEL     =      941.9822  HBOND      =        0.0000
 1-4 VDW =      194.5478  1-4 EEL =   -11322.1958  RESTRAINT  =        0.0000


   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    700      -9.3941E+03     2.4497E-01     4.9930E+00     C4       2136

 BOND    =        0.9663  ANGLE   =       33.9928  DIHED      =     1900.2484
 VDWAALS =    -1140.6768  EEL     =      938.7997  HBOND      =        0.0000
 1-4 VDW =      194.5170  1-4 EEL =   -11321.9213  RESTRAINT  =        0.0000


   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    800      -9.3970E+03     3.4093E-01     3.3504E+00     C2       2225

 BOND    =        1.0353  ANGLE   =       34.3253  DIHED      =     1900.0276
 VDWAALS =    -1141.2051  EEL     =      936.1751  HBOND      =        0.0000
 1-4 VDW =      194.5630  1-4 EEL =   -11321.9605  RESTRAINT  =        0.0000


   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    900      -9.4012E+03     4.1478E-01     5.3023E+00     H42      2138

 BOND    =        1.4918  ANGLE   =       35.5669  DIHED      =     1900.0088
 VDWAALS =    -1142.7518  EEL     =      931.5249  HBOND      =        0.0000
 1-4 VDW =      194.5022  1-4 EEL =   -11321.5246  RESTRAINT  =        0.0000


   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
   1000      -9.4108E+03     7.9749E-02     1.5375E+00     O3       1840

 BOND    =        0.8443  ANGLE   =       34.2584  DIHED      =     1900.3562
 VDWAALS =    -1143.1410  EEL     =      924.5094  HBOND      =        0.0000
 1-4 VDW =      194.3872  1-4 EEL =   -11321.9998  RESTRAINT  =        0.0000


  Maximum number of minimization cycles reached.


                    FINAL RESULTS



   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
   1000      -9.4108E+03     7.9749E-02     1.5375E+00     O3       1840

 BOND    =        0.8443  ANGLE   =       34.2584  DIHED      =     1900.3562
 VDWAALS =    -1143.1410  EEL     =      924.5094  HBOND      =        0.0000
 1-4 VDW =      194.3872  1-4 EEL =   -11321.9998  RESTRAINT  =        0.0000
--------------------------------------------------------------------------------
   5.  TIMINGS
--------------------------------------------------------------------------------

|  NonSetup CPU Time in Major Routines:
|
|     Routine           Sec        %
|     ------------------------------
|     Nonbond           0.69   80.37
|     Bond              0.00    0.00
|     Angle             0.00    0.00
|     Dihedral          0.00    0.00
|     Shake             0.00    0.00
|     Other             0.17   19.63
|     ------------------------------
|     Total             0.86

|  PME Nonbond Pairlist CPU Time:
|
|     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:
|
|     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:
|
|     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

|  Setup CPU time:            0.37 seconds
|  NonSetup CPU time:         0.86 seconds
|  Total CPU time:            1.22 seconds     0.00 hours

|  Setup wall time:           0    seconds
|  NonSetup wall time:        1    seconds
|  Total wall time:           1    seconds     0.00 hours
