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

| PMEMD implementation of SANDER, Release 12

| Run on 07/21/2014 at 16:12:22

  [-O]verwriting output

File Assignments:
|   MDIN: /home/l.gontrani/sndi/vol0.sndi                                       
|  MDOUT: mdout                                                                 
| INPCRD: min.crdo                                                              
|   PARM: CHOFOR.top                                                            
| RESTRT: restrt                                                                
|   REFC: refc                                                                  
|  MDVEL: mdvel                                                                 
|   MDEN: mden                                                                  
|  MDCRD: mdcrd                                                                 
| MDINFO: mdinfo                                                                


 Here is the input file:

PEO BMIMPF6 1:100 NVT a 50K                                                    
 &cntrl                                                                        
  imin   = 0,                                                                  
  irest  = 1,                                                                  
  ntx    = 5,                                                                  
  ntb    = 1,                                                                  
  cut    = 8,                                                                  
  ntr    = 0,                                                                  
  ntc    = 2,                                                                  
  ntf    = 2,                                                                  
  tempi  = 0.0,                                                                
  temp0  = 50.0,                                                               
  ntt    = 1,                                                                  
  ioutfm = 1,                                                                  
  nstlim = 40000, dt = 0.001                                                   
  ntpr = 100, ntwx = 100, ntwr = 100                                           
 &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:      2
|           CUDA Device ID in use:      0
|                CUDA Device Name: Tesla S2050
|     CUDA Device Global Mem Size:   2687 MB
| CUDA Device Num Multiprocessors:     14
|           CUDA Device Core Freq:   1.15 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 =    23.521

| New format PARM file being parsed.
| Version =    1.000 Date = 07/21/14 Time = 13:14:55

| 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  =   12500 NTYPES =       9 NBONH =       0 MBONA  =   11500
 NTHETH =       0 MTHETA =   20000 NPHIH =       0 MPHIA  =   25000
 NHPARM =       0 NPARM  =       0 NNB   =   56500 NRES   =    1000
 NBONA  =   11500 NTHETA =   20000 NPHIA =   25000 NUMBND =       8
 NUMANG =      12 NPTRA  =       5 NATYP =       9 NPHB   =       0
 IFBOX  =       1 NMXRS  =      21 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

| Coordinate Index Table dimensions:    10   10   10
| Direct force subcell size =     4.7064    4.7043    4.7116

     BOX TYPE: RECTILINEAR

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

                                                                                

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    =     100, ntrx    =       1, ntwr    =     100
     iwrap   =       0, ntwx    =     100, ntwv    =       0, ntwe    =       0
     ioutfm  =       1, 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  =     40000, nscm    =      1000, nrespa  =         1
     t       =   0.00000, dt      =   0.00100, vlimit  =  -1.00000

Berendsen (weak-coupling) temperature regulation:
     temp0   =  50.00000, tempi   =   0.00000, tautp   =   1.00000

SHAKE:
     ntc     =       2, jfastw  =       0
     tol     =   0.00001

| Intermolecular bonds treatment:
|     no_intermolecular_bonds =       1

| Energy averages sample interval:
|     ene_avg_sampling =     100

Ewald parameters:
     verbose =       0, ew_type =       0, nbflag  =       1, use_pme =       1
     vdwmeth =       1, eedmeth =       1, netfrc  =       1
     Box X =   47.064   Box Y =   47.043   Box Z =   47.116
     Alpha =   90.000   Beta  =   90.000   Gamma =   90.000
     NFFT1 =   48       NFFT2 =   48       NFFT3 =   48
     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 =     6.500 ps

 
 Number of triangulated 3-point waters found:        0

     Sum of charges from parm topology file =   0.00149987
     Forcing neutrality...

| Dynamic Memory, Types Used:
| Reals              435534
| Integers           980596

| Nonbonded Pairs Initial Allocation:     2087812

| GPU memory information (estimate):
| KB of GPU memory in use:     38541
| KB of CPU memory in use:     17541

--------------------------------------------------------------------------------
   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
|---------------------------------------------------
