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

| PMEMD implementation of SANDER, Release 12

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

  [-O]verwriting output

File Assignments:
|   MDIN: min_1.in                                                              
|  MDOUT: min_1.out                                                             
| INPCRD: ./acetone.crd                                                         
|   PARM: ./acetone.top                                                         
| RESTRT: min_1.rst                                                             
|   REFC: ./acetone.crd                                                         
|  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,                                                    
   ntr=1, restraint_wt=5.0, restraintmask='!@H=',                              
 &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     =       1
     restraint_wt =   5.00000

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

    LOADING THE CONSTRAINED ATOMS AS GROUPS


   5.  REFERENCE ATOM COORDINATES

  ACT                                                                             
     Mask !@H=; matches  1588 atoms

--------------------------------------------------------------------------------
   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              226134
| Integers           301315

| Nonbonded Pairs Initial Allocation:      663089

| GPU memory information (estimate):
| KB of GPU memory in use:     11309
| KB of CPU memory in use:      7109

--------------------------------------------------------------------------------
   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      -9.1778E+03     8.2335E+00     3.1082E+01     C2       1955

 BOND    =      172.7559  ANGLE   =       84.4788  DIHED      =     1890.3281
 VDWAALS =    -1134.1312  EEL     =      959.7406  HBOND      =        0.0000
 1-4 VDW =      200.9660  1-4 EEL =   -11351.9134  RESTRAINT  =        0.0000


   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    100      -9.3768E+03     4.9615E-02     3.5665E-01     C2          5

 BOND    =        0.7765  ANGLE   =       34.6095  DIHED      =     1900.0053
 VDWAALS =    -1135.9406  EEL     =      950.5683  HBOND      =        0.0000
 1-4 VDW =      193.9610  1-4 EEL =   -11322.1816  RESTRAINT  =        1.3621
 EAMBER  =    -9378.2016


   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    200      -9.3770E+03     3.9731E-02     2.5341E-01     C2       1755

 BOND    =        0.7964  ANGLE   =       34.5776  DIHED      =     1899.8158
 VDWAALS =    -1135.9375  EEL     =      950.3623  HBOND      =        0.0000
 1-4 VDW =      194.0864  1-4 EEL =   -11322.0678  RESTRAINT  =        1.4151
 EAMBER  =    -9378.3668


   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    300      -9.3770E+03     6.8494E-03     7.9944E-02     H11      2122

 BOND    =        0.7920  ANGLE   =       34.4834  DIHED      =     1899.8121
 VDWAALS =    -1135.9612  EEL     =      950.4154  HBOND      =        0.0000
 1-4 VDW =      194.0981  1-4 EEL =   -11322.0884  RESTRAINT  =        1.4384
 EAMBER  =    -9378.4485


   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    400      -9.3770E+03     1.2266E-02     1.5863E-01     C2       2315

 BOND    =        0.7895  ANGLE   =       34.4694  DIHED      =     1899.7992
 VDWAALS =    -1135.9815  EEL     =      950.3794  HBOND      =        0.0000
 1-4 VDW =      194.0870  1-4 EEL =   -11322.0483  RESTRAINT  =        1.4661
 EAMBER  =    -9378.5053


   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    500      -9.3771E+03     1.0630E-02     1.4162E-01     C2       2315

 BOND    =        0.7877  ANGLE   =       34.4637  DIHED      =     1899.7890
 VDWAALS =    -1135.9998  EEL     =      950.3472  HBOND      =        0.0000
 1-4 VDW =      194.0778  1-4 EEL =   -11322.0159  RESTRAINT  =        1.4913
 EAMBER  =    -9378.5503

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

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


   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    600      -9.3771E+03     4.5047E-03     9.1310E-02     O3       1960

 BOND    =        0.7809  ANGLE   =       34.4490  DIHED      =     1899.7630
 VDWAALS =    -1136.0658  EEL     =      950.2522  HBOND      =        0.0000
 1-4 VDW =      194.0554  1-4 EEL =   -11321.9351  RESTRAINT  =        1.5970
 EAMBER  =    -9378.7004

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

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

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


                    FINAL RESULTS



   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    698      -9.3771E+03     3.1411E-03     3.0726E-02     C2       2955

 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  =        1.6050
 EAMBER  =    -9378.7097

     ***** REPEATED LINMIN FAILURE *****
--------------------------------------------------------------------------------
   5.  TIMINGS
--------------------------------------------------------------------------------

|  NonSetup CPU Time in Major Routines:
|
|     Routine           Sec        %
|     ------------------------------
|     Nonbond           0.49   82.00
|     Bond              0.00    0.00
|     Angle             0.00    0.00
|     Dihedral          0.00    0.00
|     Shake             0.00    0.00
|     Other             0.11   18.00
|     ------------------------------
|     Total             0.60

|  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:            0.54 seconds
|  NonSetup CPU time:         0.60 seconds
|  Total CPU time:            1.14 seconds     0.00 hours

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