Re: [AMBER] NaN error in .rst files - UPDATE

From: peker milas <pekermilas.gmail.com>
Date: Thu, 27 Jan 2011 10:07:31 -0500

Hi Marek,

Just to let you know, i started your run couple minutes ago. I will
keep you informed.

best
peker

2011/1/26 Marek Maly <marek.maly.ujep.cz>:
> Hi Ross and All,
>
> here are some system specifications. Moreover I already confirmed
> reproducibility of the given NaN error on another PC equipped with
> GTX 470 GPU (with identical architecture as the first PC where I originally
> discovered the error). On the other hand the error was NOT
> reproduced on our Tesla C2050 ! - see below.
>
> I am really curious if you or anyone else will be able to reproduce NaN
> error on  GTX 470 GPU system,
> using my previously posted input files.
>
>
>   Best wishes,
>
>     Marek
>
>
>
>
> ****************GTX 470 MACHINES*****************
>
> SW:
>
> OS spec:
>
> Linux 2.6.34-12-desktop  (OpenSuSE)
>
> GNU Amber11 compilation with bugfixes applied up to bugfix 12.
>
> gcc version 4.5.0 20100604 [gcc-4_5-branch revision 160292] (SUSE Linux)
>
> (obtained with command gcc -v or gfortran -v)
>
> CUDA spec:
> devdriver_3.2_linux_64_260.24.run
> cudatoolkit_3.2.16_linux_64_suse11.2.run
> gpucomputingsdk_3.2.16_linux.run
>
> Regarding to HW, I know for this moment that PCs are equipped with
> six-core AMD CPUs and GTX 470 GPUs,
> I will learn the details from the responsible guy and will send during
> tomorrow.
>
> ****************TESLA MACHINE*****************
>
> SW:
>
> OS spec:
>
> Ubuntu 10.04.1 LTS (Ubuntu server)
>
>
> GNU Amber11 compilation with bugfixes applied up to bugfix 11 (for the
> moment).
>
> gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5)
>
> CUDA spec:
>
> devdriver_3.2_linux_64_260.19.26.run
> cudatoolkit_3.2.16_linux_64_ubuntu10.04.run
>
> HW:
>
> CASE: COOLERMASTER DOMINATOR /Xcalade
> CPU: AMD Phenom II X4 955 Black Edition (3,2GHz, s. AM3, 125W, C3) BOX
> HDD: Seagate Barracuda 7200.12, 3,5" SATA II, 32MB - 1TB
> MB: Asus M4N98TD EVO - nForce 980a, DDR3, s. AM3, ATX
> RAM: Corsair 4x2GB DDR3 1600MHz CL8 (CMP4GX3M2A1600C8)
> POWER: CoolerMaster Silent Pro Gold Active - 700W
> 2 x TESLA C2050
>
> ############ GXT 470 OUTPUT #################
> ############ GXT 470 OUTPUT #################
> ############ GXT 470 OUTPUT #################
> ############ GXT 470 OUTPUT #################
> ############ GXT 470 OUTPUT #################
>
>           -------------------------------------------------------
>           Amber 11 SANDER                              2010
>           -------------------------------------------------------
>
> | PMEMD implementation of SANDER, Release 11
>
> | Run on 01/26/2011 at 17:52:17
>
>   [-O]verwriting output
>
> File Assignments:
> |   MDIN: equil_G4malTRI_10BIL.in
> |  MDOUT: equil8_G4malTRI_10BIL.out
> | INPCRD: equil7_G4malTRI_10BIL.rst
> |   PARM: G4malTRI_10BIL.prmtop
> | RESTRT: equil8_G4malTRI_10BIL.rst
> |   REFC: refc
> |  MDVEL: mdvel
> |   MDEN: mden
> |  MDCRD: equil8_G4malTRI_10BIL.mdcrd
> | MDINFO: mdinfo
>
>
>  Here is the input file:
>
> heat ras-raf
>  &cntrl
>   imin=0,irest=1,ntx=5,
>   nstlim=250000,dt=0.002,
>   ntc=2,ntf=2,
>   cut=10.0, ntb=2, ntp=1, taup=1.0,
>   ntpr=5000, ntwx=5000,
>   ntt=3, gamma_ln=2.0, ig=676075,
>     temp0=298,
>  /
>
>
>
>
> |--------------------- INFORMATION ----------------------
> | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
> |                      Version 2.1
> |
> |                      12/20/2010
> |
> |
> | 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:
> |      [SPDP] - Hybrid Single/Double Precision (Default).
> |
> |--------------------------------------------------------
>
> |------------------- GPU DEVICE INFO --------------------
> |
> |   CUDA Capable Devices Detected:      1
> |           CUDA Device ID in use:      0
> |                CUDA Device Name: GeForce GTX 470
> |     CUDA Device Global Mem Size:   1279 MB
> | CUDA Device Num Multiprocessors:     14
> |           CUDA Device Core Freq:   1.22 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 =    43.365
>
> | New format PARM file being parsed.
> | Version =    1.000 Date = 01/21/11 Time = 18:45:59
>
> | 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  =   92246 NTYPES =      16 NBONH =   89280 MBONA  =    2945
>  NTHETH =    6302 MTHETA =    4240 NPHIH =   11120 MPHIA  =    8029
>  NHPARM =       0 NPARM  =       0 NNB   =  147846 NRES   =   29261
>  NBONA  =    2945 NTHETA =    4240 NPHIA =    8029 NUMBND =      33
>  NUMANG =      67 NPTRA  =      38 NATYP =      25 NPHB   =       1
>  IFBOX  =       2 NMXRS  =      77 IFCAP =       0 NEXTRA =       0
>  NCOPY  =       0
>
> | Coordinate Index Table dimensions:    17   17   17
> | Direct force subcell size =     6.2484    6.2484    6.2484
>
>      BOX TYPE: TRUNCATED OCTAHEDRON
>
> --------------------------------------------------------------------------------
>    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    =    5000, ntrx    =       1, ntwr
> =     500
>      iwrap   =       0, ntwx    =    5000, ntwv    =       0, ntwe
> =       0
>      ioutfm  =       0, ntwprt  =       0, idecomp =       0,
> rbornstat=      0
>
> Potential function:
>      ntf     =       2, ntb     =       2, 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  =    250000, nscm    =      1000, nrespa  =         1
>      t       =   0.00000, dt      =   0.00200, vlimit  =  -1.00000
>
> Langevin dynamics temperature regulation:
>      ig      =  676075
>      temp0   = 298.00000, tempi   =   0.00000, gamma_ln=   2.00000
>
> Pressure regulation:
>      ntp     =       1
>      pres0   =   1.00000, comp    =  44.60000, taup    =   1.00000
>
> SHAKE:
>      ntc     =       2, jfastw  =       0
>      tol     =   0.00001
>
> | Intermolecular bonds treatment:
> |     no_intermolecular_bonds =       1
>
> | Energy averages sample interval:
> |     ene_avg_sampling =    5000
>
> Ewald parameters:
>      verbose =       0, ew_type =       0, nbflag  =       1, use_pme
> =       1
>      vdwmeth =       1, eedmeth =       1, netfrc  =       1
>      Box X =  106.223   Box Y =  106.223   Box Z =  106.223
>      Alpha =  109.471   Beta  =  109.471   Gamma =  109.471
>      NFFT1 =  108       NFFT2 =  108       NFFT3 =  108
>      Cutoff=   10.000   Tol   =0.100E-04
>      Ewald Coefficient =  0.27511
>      Interpolation order =    4
>
> --------------------------------------------------------------------------------
>    3.  ATOMIC COORDINATES AND VELOCITIES
> --------------------------------------------------------------------------------
>
>
>  begin time read from input coords =  3700.000 ps
>
>
>  Number of triangulated 3-point waters found:    28820
>
>      Sum of charges from parm topology file =  -0.00266701
>      Forcing neutrality...
>
> | Dynamic Memory, Types Used:
> | Reals             2846082
> | Integers          2613755
>
> | Nonbonded Pairs Initial Allocation:    27902108
>
> | GPU memory information:
> | KB of GPU memory in use:    876823
> | KB of CPU memory in use:     77099
>
> --------------------------------------------------------------------------------
>    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 =     5000   TIME(PS) =    3710.000  TEMP(K) =   298.54  PRESS =
> 19.7
>  Etot   =   -208138.5945  EKtot   =     55606.0703  EPtot      =
> -263744.6648
>  BOND   =     12770.3337  ANGLE   =      5327.0090  DIHED      =
> 1796.1712
>  1-4 NB =      1220.6297  1-4 EEL =     32614.9838  VDWAALS    =
> 44968.0029
>  EELEC  =   -362441.7951  EHBOND  =         0.0000  RESTRAINT  =
> 0.0000
>  EKCMT  =     25890.2734  VIRIAL  =     25498.7611  VOLUME     =
> 920970.7237
>                                                     Density    =
> 1.0185
>  ------------------------------------------------------------------------------
>
>
>  NSTEP =    10000   TIME(PS) =    3720.000  TEMP(K) =   296.22  PRESS =
> 73.8
>  Etot   =   -208072.6867  EKtot   =     55172.7422  EPtot      =
> -263245.4289
>  BOND   =     12797.2804  ANGLE   =      5280.3633  DIHED      =
> 1793.7009
>  1-4 NB =      1236.9252  1-4 EEL =     32530.0890  VDWAALS    =
> 45147.6190
>  EELEC  =   -362031.4066  EHBOND  =         0.0000  RESTRAINT  =
> 0.0000
>  EKCMT  =     25827.2976  VIRIAL  =     24357.5606  VOLUME     =
> 921836.9062
>                                                     Density    =
> 1.0176
>  ------------------------------------------------------------------------------
>
>
>  NSTEP =    15000   TIME(PS) =    3730.000  TEMP(K) =   299.32  PRESS =
> 133.8
>  Etot   =   -207140.0864  EKtot   =     55750.0508  EPtot      =
> -262890.1372
>  BOND   =     12813.3463  ANGLE   =      5316.1231  DIHED      =
> 1777.2270
>  1-4 NB =      1214.8564  1-4 EEL =     32504.7227  VDWAALS    =
> 45134.9078
>  EELEC  =   -361651.3206  EHBOND  =         0.0000  RESTRAINT  =
> 0.0000
>  EKCMT  =     26061.3868  VIRIAL  =     23397.2429  VOLUME     =
> 922304.1794
>                                                     Density    =
> 1.0171
>  ------------------------------------------------------------------------------
>
>
>  NSTEP =    20000   TIME(PS) =    3740.000  TEMP(K) =      NaN  PRESS
> =     NaN
>  Etot   =            NaN  EKtot   =            NaN  EPtot
> =            NaN
>  BOND   =         0.0000  ANGLE   =    795708.3759  DIHED      =
> 0.0000
>  1-4 NB =         0.0000  1-4 EEL =         0.0000  VDWAALS    =
> -1408.8764
>  EELEC  =            NaN  EHBOND  =         0.0000  RESTRAINT  =
> 0.0000
>  EKCMT  =         0.0000  VIRIAL  =            NaN  VOLUME
> =            NaN
>                                                     Density
> =            NaN
>  ------------------------------------------------------------------------------
>
>
>  NSTEP =    25000   TIME(PS) =    3750.000  TEMP(K) =      NaN  PRESS
> =     NaN
>  Etot   =            NaN  EKtot   =            NaN  EPtot
> =            NaN
>  BOND   =         0.0000  ANGLE   =    795708.3759  DIHED      =
> 0.0000
>  1-4 NB =         0.0000  1-4 EEL =         0.0000  VDWAALS    =
> -1408.8764
>  EELEC  =            NaN  EHBOND  =         0.0000  RESTRAINT  =
> 0.0000
>  EKCMT  =         0.0000  VIRIAL  =            NaN  VOLUME
> =            NaN
>                                                     Density
> =            NaN
>  ------------------------------------------------------------------------------
>
>
>  NSTEP =    30000   TIME(PS) =    3760.000  TEMP(K) =      NaN  PRESS
> =     NaN
>  Etot   =            NaN  EKtot   =            NaN  EPtot
> =            NaN
>  BOND   =         0.0000  ANGLE   =    795708.3759  DIHED      =
> 0.0000
>  1-4 NB =         0.0000  1-4 EEL =         0.0000  VDWAALS    =
> -1408.8764
>  EELEC  =            NaN  EHBOND  =         0.0000  RESTRAINT  =
> 0.0000
>  EKCMT  =         0.0000  VIRIAL  =            NaN  VOLUME
> =            NaN
>                                                     Density
> =            NaN
>  ------------------------------------------------------------------------------
>
> ############ TESLA OUTPUT #################
> ############ TESLA OUTPUT #################
> ############ TESLA OUTPUT #################
> ############ TESLA OUTPUT #################
> ############ TESLA OUTPUT #################
>
>
>           -------------------------------------------------------
>           Amber 11 SANDER                              2010
>           -------------------------------------------------------
>
> | PMEMD implementation of SANDER, Release 11
>
> | Run on 01/26/2011 at 21:54:14
>
>   [-O]verwriting output
>
> File Assignments:
> |   MDIN: equil_G4malTRI_10BIL.in
> |  MDOUT: equil8_G4malTRI_10BIL.out
> | INPCRD: equil7_G4malTRI_10BIL.rst
> |   PARM: G4malTRI_10BIL.prmtop
> | RESTRT: equil8_G4malTRI_10BIL.rst
> |   REFC: refc
> |  MDVEL: mdvel
> |   MDEN: mden
> |  MDCRD: equil8_G4malTRI_10BIL.mdcrd
> | MDINFO: mdinfo
>
>
>  Here is the input file:
>
> heat ras-raf
>  &cntrl
>   imin=0,irest=1,ntx=5,
>   nstlim=250000,dt=0.002,
>   ntc=2,ntf=2,
>   cut=10.0, ntb=2, ntp=1, taup=1.0,
>   ntpr=5000, ntwx=5000,
>   ntt=3, gamma_ln=2.0, ig=676075,
>     temp0=298,
>  /
>
>
>
>
> |--------------------- INFORMATION ----------------------
> | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
> |
> | 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:
> |      [SPDP] - Hybrid Single/Double Precision (Default).
> |
> |--------------------------------------------------------
>
> |------------------- GPU DEVICE INFO --------------------
> |
> |   CUDA Capable Devices Detected:      2
> |           CUDA Device ID in use:      1
> |                CUDA Device Name: Tesla C2050
> |     CUDA Device Global Mem Size:   3071 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 =    43.365
>
> | New format PARM file being parsed.
> | Version =    1.000 Date = 01/21/11 Time = 18:45:59
>
> | 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  =   92246 NTYPES =      16 NBONH =   89280 MBONA  =    2945
>  NTHETH =    6302 MTHETA =    4240 NPHIH =   11120 MPHIA  =    8029
>  NHPARM =       0 NPARM  =       0 NNB   =  147846 NRES   =   29261
>  NBONA  =    2945 NTHETA =    4240 NPHIA =    8029 NUMBND =      33
>  NUMANG =      67 NPTRA  =      38 NATYP =      25 NPHB   =       1
>  IFBOX  =       2 NMXRS  =      77 IFCAP =       0 NEXTRA =       0
>  NCOPY  =       0
>
> | Coordinate Index Table dimensions:    17   17   17
> | Direct force subcell size =     6.2484    6.2484    6.2484
>
>      BOX TYPE: TRUNCATED OCTAHEDRON
>
> --------------------------------------------------------------------------------
>    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    =    5000, ntrx    =       1, ntwr
> =     500
>      iwrap   =       0, ntwx    =    5000, ntwv    =       0, ntwe
> =       0
>      ioutfm  =       0, ntwprt  =       0, idecomp =       0,
> rbornstat=      0
>
> Potential function:
>      ntf     =       2, ntb     =       2, 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  =    250000, nscm    =      1000, nrespa  =         1
>      t       =   0.00000, dt      =   0.00200, vlimit  =  -1.00000
>
> Langevin dynamics temperature regulation:
>      ig      =  676075
>      temp0   = 298.00000, tempi   =   0.00000, gamma_ln=   2.00000
>
> Pressure regulation:
>      ntp     =       1
>      pres0   =   1.00000, comp    =  44.60000, taup    =   1.00000
>
> SHAKE:
>      ntc     =       2, jfastw  =       0
>      tol     =   0.00001
>
> | Intermolecular bonds treatment:
> |     no_intermolecular_bonds =       1
>
> | Energy averages sample interval:
> |     ene_avg_sampling =    5000
>
> Ewald parameters:
>      verbose =       0, ew_type =       0, nbflag  =       1, use_pme
> =       1
>      vdwmeth =       1, eedmeth =       1, netfrc  =       1
>      Box X =  106.223   Box Y =  106.223   Box Z =  106.223
>      Alpha =  109.471   Beta  =  109.471   Gamma =  109.471
>      NFFT1 =  108       NFFT2 =  108       NFFT3 =  108
>      Cutoff=   10.000   Tol   =0.100E-04
>      Ewald Coefficient =  0.27511
>      Interpolation order =    4
>
> --------------------------------------------------------------------------------
>    3.  ATOMIC COORDINATES AND VELOCITIES
> --------------------------------------------------------------------------------
>
>
>  begin time read from input coords =  3700.000 ps
>
>
>  Number of triangulated 3-point waters found:    28820
>
>      Sum of charges from parm topology file =  -0.00266701
>      Forcing neutrality...
>
> | Dynamic Memory, Types Used:
> | Reals             2846082
> | Integers          2613755
>
> | Nonbonded Pairs Initial Allocation:    27902108
>
> --------------------------------------------------------------------------------
>    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 =     5000   TIME(PS) =    3710.000  TEMP(K) =   298.17  PRESS =
> -65.0
>  Etot   =   -208105.5602  EKtot   =     55536.2500  EPtot      =
> -263641.8102
>  BOND   =     12866.3112  ANGLE   =      5342.0912  DIHED      =
> 1767.6154
>  1-4 NB =      1260.5860  1-4 EEL =     32577.8341  VDWAALS    =
> 45096.1019
>  EELEC  =   -362552.3502  EHBOND  =         0.0000  RESTRAINT  =
> 0.0000
>  EKCMT  =     25784.6613  VIRIAL  =     27079.4346  VOLUME     =
> 922977.4720
>                                                     Density    =
> 1.0163
>  ------------------------------------------------------------------------------
>
>
>  NSTEP =    10000   TIME(PS) =    3720.000  TEMP(K) =   298.45  PRESS =
> -21.0
>  Etot   =   -207729.1303  EKtot   =     55589.4570  EPtot      =
> -263318.5874
>  BOND   =     12890.8807  ANGLE   =      5253.2612  DIHED      =
> 1777.9787
>  1-4 NB =      1222.3407  1-4 EEL =     32539.5469  VDWAALS    =
> 45053.4545
>  EELEC  =   -362056.0500  EHBOND  =         0.0000  RESTRAINT  =
> 0.0000
>  EKCMT  =     25763.3611  VIRIAL  =     26182.4102  VOLUME     =
> 922146.5473
>                                                     Density    =
> 1.0172
>  ------------------------------------------------------------------------------
>
>
>  NSTEP =    15000   TIME(PS) =    3730.000  TEMP(K) =   298.37  PRESS =
> 98.2
>  Etot   =   -207996.7778  EKtot   =     55573.0195  EPtot      =
> -263569.7973
>  BOND   =     12785.0173  ANGLE   =      5270.3883  DIHED      =
> 1784.1405
>  1-4 NB =      1220.4520  1-4 EEL =     32552.7635  VDWAALS    =
> 45295.2640
>  EELEC  =   -362477.8230  EHBOND  =         0.0000  RESTRAINT  =
> 0.0000
>  EKCMT  =     25963.8604  VIRIAL  =     24009.0863  VOLUME     =
> 922094.0380
>                                                     Density    =
> 1.0173
>  ------------------------------------------------------------------------------
>
>
>  NSTEP =    20000   TIME(PS) =    3740.000  TEMP(K) =   298.20  PRESS =
> 67.7
>  Etot   =   -208293.8436  EKtot   =     55542.7656  EPtot      =
> -263836.6093
>  BOND   =     12872.9016  ANGLE   =      5363.9036  DIHED      =
> 1795.2137
>  1-4 NB =      1213.2018  1-4 EEL =     32466.5915  VDWAALS    =
> 45424.6127
>  EELEC  =   -362973.0342  EHBOND  =         0.0000  RESTRAINT  =
> 0.0000
>  EKCMT  =     25522.4362  VIRIAL  =     24176.4890  VOLUME     =
> 921096.1611
>                                                     Density    =
> 1.0184
>  ------------------------------------------------------------------------------
>
>
>  NSTEP =    25000   TIME(PS) =    3750.000  TEMP(K) =   299.33  PRESS =
> -129.9
>  Etot   =   -207342.5575  EKtot   =     55752.0117  EPtot      =
> -263094.5692
>  BOND   =     12831.1293  ANGLE   =      5359.5763  DIHED      =
> 1781.3044
>  1-4 NB =      1241.1887  1-4 EEL =     32550.6750  VDWAALS    =
> 44670.0979
>  EELEC  =   -361528.5407  EHBOND  =         0.0000  RESTRAINT  =
> 0.0000
>  EKCMT  =     25933.6779  VIRIAL  =     28525.6386  VOLUME     =
> 923959.6257
>                                                     Density    =
> 1.0153
>  ------------------------------------------------------------------------------
>
>
>  NSTEP =    30000   TIME(PS) =    3760.000  TEMP(K) =   299.23  PRESS =
> -48.6
>  Etot   =   -207514.9903  EKtot   =     55734.1758  EPtot      =
> -263249.1661
>  BOND   =     12685.1313  ANGLE   =      5395.4329  DIHED      =
> 1767.0411
>  1-4 NB =      1226.7051  1-4 EEL =     32517.0993  VDWAALS    =
> 45071.9541
>  EELEC  =   -361912.5299  EHBOND  =         0.0000  RESTRAINT  =
> 0.0000
>  EKCMT  =     26018.3035  VIRIAL  =     26987.2669  VOLUME     =
> 922634.0169
>                                                     Density    =
> 1.0167
>  ------------------------------------------------------------------------------
>
>
>
>
>
>
>
>
> Dne Wed, 26 Jan 2011 17:45:07 +0100 Ross Walker <ross.rosswalker.co.uk>
> napsal/-a:
>
>> Hi Marek,
>>
>> Can you please send me the exact input files for the run that reproduces
>> the
>> error you see. Specifically the one that sets the ig value to the setting
>> that causes the issue. My suspicion is, given this is reproducible, that
>> something is going crazy in the random number generator. I assume these
>> are
>> all ntt=3 runs.
>>
>> Can you also include the exact nvcc compiler version, driver version,
>> card
>> specs (deviceQuery will give this, since I need bios revision etc) as
>> well
>> as the exact compiler and version you used to build pmemd.cuda, for
>> example
>> the gcc / gfortran version numbers.
>>
>> The interesting thing will be if this problem is reproducible on an
>> identical system to the one you see it on. I.e. the exact same model
>> card,
>> driver, compiler versions etc. If it is then we can make progress pretty
>> quickly to fix it. If it isn't then well errrr.... ugh...
>>
>> All the best
>> Ross
>>
>>> -----Original Message-----
>>> From: Marek Maly [mailto:marek.maly.ujep.cz]
>>> Sent: Wednesday, January 26, 2011 8:23 AM
>>> To: AMBER Mailing List
>>> Subject: Re: [AMBER] NaN error in .rst files
>>>
>>> Hello All,
>>>
>>> it seems that the error is reproducible as indicated
>>> Peker sooner - see data below (the verification test was done on the
>>> same
>>> machine as the original one, with the same random seed) (although that
>>> restarted simulation with ig=-1
>>> helped here to continue simulation from the critical point, but of
>>> course,
>>> this is not the systematic solution and the given error might occure
>>> also
>>> in
>>> future of this run ...).
>>>
>>> So now I will try to verify this error
>>>
>>> #1 - on another machine (again with GTX 470)
>>>
>>> #2 - on TESLA C2050, unfortunately here I have no bugfix 12 applied, but
>>> box is not small ( 106.2227312 106.2227312 106.2227312 109.4712190
>>> 109.4712190 109.4712190 ) so
>>> there shouldn.t be problems with 10 A cutoff or am I wrong ?. Anyway I
>>> can
>>> later recompile with the
>>> bugfix 12 as well.
>>>
>>> #3
>>> on CPUs which can also help to find out the source of the error.
>>>
>>> When I have some results I will post them here.
>>>
>>> Best wishes,
>>>
>>>       Marek
>>>
>>>
>>>
>>> ############### ORIGINAL RUN ##########################
>>> ############### ORIGINAL RUN ##########################
>>> ############### ORIGINAL RUN ##########################
>>> ############### ORIGINAL RUN ##########################
>>> ############### ORIGINAL RUN ##########################
>>>
>>>
>>>
>>>            -------------------------------------------------------
>>>            Amber 11 SANDER                              2010
>>>            -------------------------------------------------------
>>>
>>> | PMEMD implementation of SANDER, Release 11
>>>
>>> | Run on 01/24/2011 at 00:12:00
>>>
>>>    [-O]verwriting output
>>>
>>> File Assignments:
>>> |   MDIN: equil_G4malTRI_10BIL.in
>>> |  MDOUT: equil8_G4malTRI_10BIL.out
>>> | INPCRD: equil7_G4malTRI_10BIL.rst
>>> |   PARM: G4malTRI_10BIL.prmtop
>>> | RESTRT: equil8_G4malTRI_10BIL.rst
>>> |   REFC: refc
>>> |  MDVEL: mdvel
>>> |   MDEN: mden
>>> |  MDCRD: equil8_G4malTRI_10BIL.mdcrd
>>> | MDINFO: mdinfo
>>>
>>>
>>>   Here is the input file:
>>>
>>> heat ras-raf
>>>   &cntrl
>>>    imin=0,irest=1,ntx=5,
>>>    nstlim=250000,dt=0.002,
>>>    ntc=2,ntf=2,
>>>    cut=10.0, ntb=2, ntp=1, taup=1.0,
>>>    ntpr=5000, ntwx=5000,
>>>    ntt=3, gamma_ln=2.0, ig=-1,
>>>      temp0=298,
>>>   /
>>>
>>>
>>>
>>>
>>> |--------------------- INFORMATION ----------------------
>>> | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
>>> |                      Version 2.1
>>> |
>>> |                      12/20/2010
>>> |
>>> |
>>> | 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:
>>> |      [SPDP] - Hybrid Single/Double Precision (Default).
>>> |
>>> |--------------------------------------------------------
>>>
>>> |------------------- GPU DEVICE INFO --------------------
>>> |
>>> |   CUDA Capable Devices Detected:      1
>>> |           CUDA Device ID in use:      0
>>> |                CUDA Device Name: GeForce GTX 470
>>> |     CUDA Device Global Mem Size:   1279 MB
>>> | CUDA Device Num Multiprocessors:     14
>>> |           CUDA Device Core Freq:   1.22 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 =    43.365
>>>
>>> | New format PARM file being parsed.
>>> | Version =    1.000 Date = 01/21/11 Time = 18:45:59
>>>
>>> | 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  =   92246 NTYPES =      16 NBONH =   89280 MBONA  =    2945
>>>   NTHETH =    6302 MTHETA =    4240 NPHIH =   11120 MPHIA  =    8029
>>>   NHPARM =       0 NPARM  =       0 NNB   =  147846 NRES   =   29261
>>>   NBONA  =    2945 NTHETA =    4240 NPHIA =    8029 NUMBND =      33
>>>   NUMANG =      67 NPTRA  =      38 NATYP =      25 NPHB   =       1
>>>   IFBOX  =       2 NMXRS  =      77 IFCAP =       0 NEXTRA =       0
>>>   NCOPY  =       0
>>>
>>> | Coordinate Index Table dimensions:    17   17   17
>>> | Direct force subcell size =     6.2484    6.2484    6.2484
>>>
>>>       BOX TYPE: TRUNCATED OCTAHEDRON
>>>
>>>
>> ----------------------------------------------------------------------------
>> ----
>>>     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    =    5000, ntrx    =       1, ntwr
>>> =     500
>>>       iwrap   =       0, ntwx    =    5000, ntwv    =       0, ntwe
>>> =       0
>>>       ioutfm  =       0, ntwprt  =       0, idecomp =       0,
>>> rbornstat=      0
>>>
>>> Potential function:
>>>       ntf     =       2, ntb     =       2, 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  =    250000, nscm    =      1000, nrespa  =         1
>>>       t       =   0.00000, dt      =   0.00200, vlimit  =  -1.00000
>>>
>>> Langevin dynamics temperature regulation:
>>>       ig      =  676075
>>>       temp0   = 298.00000, tempi   =   0.00000, gamma_ln=   2.00000
>>>
>>> Pressure regulation:
>>>       ntp     =       1
>>>       pres0   =   1.00000, comp    =  44.60000, taup    =   1.00000
>>>
>>> SHAKE:
>>>       ntc     =       2, jfastw  =       0
>>>       tol     =   0.00001
>>>
>>> | Intermolecular bonds treatment:
>>> |     no_intermolecular_bonds =       1
>>>
>>> | Energy averages sample interval:
>>> |     ene_avg_sampling =    5000
>>>
>>> Ewald parameters:
>>>       verbose =       0, ew_type =       0, nbflag  =       1, use_pme
>>> =       1
>>>       vdwmeth =       1, eedmeth =       1, netfrc  =       1
>>>       Box X =  106.223   Box Y =  106.223   Box Z =  106.223
>>>       Alpha =  109.471   Beta  =  109.471   Gamma =  109.471
>>>       NFFT1 =  108       NFFT2 =  108       NFFT3 =  108
>>>       Cutoff=   10.000   Tol   =0.100E-04
>>>       Ewald Coefficient =  0.27511
>>>       Interpolation order =    4
>>>
>>>
>> ----------------------------------------------------------------------------
>> ----
>>>     3.  ATOMIC COORDINATES AND VELOCITIES
>>>
>> ----------------------------------------------------------------------------
>> ----
>>>
>>>
>>>   begin time read from input coords =  3700.000 ps
>>>
>>>
>>>   Number of triangulated 3-point waters found:    28820
>>>
>>>       Sum of charges from parm topology file =  -0.00266701
>>>       Forcing neutrality...
>>>
>>> | Dynamic Memory, Types Used:
>>> | Reals             2846082
>>> | Integers          2613755
>>>
>>> | Nonbonded Pairs Initial Allocation:    27902108
>>>
>>> | GPU memory information:
>>> | KB of GPU memory in use:    876823
>>> | KB of CPU memory in use:     77099
>>>
>>>
>> ----------------------------------------------------------------------------
>> ----
>>>     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 =     5000   TIME(PS) =    3710.000  TEMP(K) =   298.54  PRESS =
>>> 19.7
>>>   Etot   =   -208138.5945  EKtot   =     55606.0703  EPtot      =
>>> -263744.6648
>>>   BOND   =     12770.3337  ANGLE   =      5327.0090  DIHED      =
>>> 1796.1712
>>>   1-4 NB =      1220.6297  1-4 EEL =     32614.9838  VDWAALS    =
>>> 44968.0029
>>>   EELEC  =   -362441.7951  EHBOND  =         0.0000  RESTRAINT  =
>>> 0.0000
>>>   EKCMT  =     25890.2734  VIRIAL  =     25498.7611  VOLUME     =
>>> 920970.7237
>>>                                                      Density    =
>>> 1.0185
>>>
>> ----------------------------------------------------------------------------
>> --
>>>
>>>
>>>   NSTEP =    10000   TIME(PS) =    3720.000  TEMP(K) =   296.22  PRESS =
>>> 73.8
>>>   Etot   =   -208072.6867  EKtot   =     55172.7422  EPtot      =
>>> -263245.4289
>>>   BOND   =     12797.2804  ANGLE   =      5280.3633  DIHED      =
>>> 1793.7009
>>>   1-4 NB =      1236.9252  1-4 EEL =     32530.0890  VDWAALS    =
>>> 45147.6190
>>>   EELEC  =   -362031.4066  EHBOND  =         0.0000  RESTRAINT  =
>>> 0.0000
>>>   EKCMT  =     25827.2976  VIRIAL  =     24357.5606  VOLUME     =
>>> 921836.9062
>>>                                                      Density    =
>>> 1.0176
>>>
>> ----------------------------------------------------------------------------
>> --
>>>
>>>
>>>   NSTEP =    15000   TIME(PS) =    3730.000  TEMP(K) =   299.32  PRESS =
>>> 133.8
>>>   Etot   =   -207140.0864  EKtot   =     55750.0508  EPtot      =
>>> -262890.1372
>>>   BOND   =     12813.3463  ANGLE   =      5316.1231  DIHED      =
>>> 1777.2270
>>>   1-4 NB =      1214.8564  1-4 EEL =     32504.7227  VDWAALS    =
>>> 45134.9078
>>>   EELEC  =   -361651.3206  EHBOND  =         0.0000  RESTRAINT  =
>>> 0.0000
>>>   EKCMT  =     26061.3868  VIRIAL  =     23397.2429  VOLUME     =
>>> 922304.1794
>>>                                                      Density    =
>>> 1.0171
>>>
>> ----------------------------------------------------------------------------
>> --
>>>
>>>
>>>   NSTEP =    20000   TIME(PS) =    3740.000  TEMP(K) =      NaN  PRESS
>>> =     NaN
>>>   Etot   =            NaN  EKtot   =            NaN  EPtot
>>> =            NaN
>>>   BOND   =         0.0000  ANGLE   =    795708.3759  DIHED      =
>>> 0.0000
>>>   1-4 NB =         0.0000  1-4 EEL =         0.0000  VDWAALS    =
>>> -1408.8764
>>>   EELEC  =            NaN  EHBOND  =         0.0000  RESTRAINT  =
>>> 0.0000
>>>   EKCMT  =         0.0000  VIRIAL  =            NaN  VOLUME
>>> =            NaN
>>>                                                      Density
>>> =            NaN
>>>
>> ----------------------------------------------------------------------------
>> --
>>>
>>>
>>>   NSTEP =    25000   TIME(PS) =    3750.000  TEMP(K) =      NaN  PRESS
>>> =     NaN
>>>   Etot   =            NaN  EKtot   =            NaN  EPtot
>>> =            NaN
>>>   BOND   =         0.0000  ANGLE   =    795708.3759  DIHED      =
>>> 0.0000
>>>   1-4 NB =         0.0000  1-4 EEL =         0.0000  VDWAALS    =
>>> -1408.8764
>>>   EELEC  =            NaN  EHBOND  =         0.0000  RESTRAINT  =
>>> 0.0000
>>>   EKCMT  =         0.0000  VIRIAL  =            NaN  VOLUME
>>> =            NaN
>>>                                                      Density
>>> =            NaN
>>>
>> ----------------------------------------------------------------------------
>> --
>>>
>>>
>>>
>>>
>>> ############### VERIFICATION RUN ######################
>>> ############### VERIFICATION RUN ######################
>>> ############### VERIFICATION RUN ######################
>>> ############### VERIFICATION RUN ######################
>>> ############### VERIFICATION RUN ######################
>>>
>>>
>>>
>>>            -------------------------------------------------------
>>>            Amber 11 SANDER                              2010
>>>            -------------------------------------------------------
>>>
>>> | PMEMD implementation of SANDER, Release 11
>>>
>>> | Run on 01/26/2011 at 15:38:33
>>>
>>>    [-O]verwriting output
>>>
>>> File Assignments:
>>> |   MDIN: equil_G4malTRI_10BIL.in
>>> |  MDOUT: equil8_G4malTRI_10BIL.out
>>> | INPCRD: equil7_G4malTRI_10BIL.rst
>>> |   PARM: G4malTRI_10BIL.prmtop
>>> | RESTRT: equil8_G4malTRI_10BIL.rst
>>> |   REFC: refc
>>> |  MDVEL: mdvel
>>> |   MDEN: mden
>>> |  MDCRD: equil8_G4malTRI_10BIL.mdcrd
>>> | MDINFO: mdinfo
>>>
>>>
>>>   Here is the input file:
>>>
>>> heat ras-raf
>>>   &cntrl
>>>    imin=0,irest=1,ntx=5,
>>>    nstlim=250000,dt=0.002,
>>>    ntc=2,ntf=2,
>>>    cut=10.0, ntb=2, ntp=1, taup=1.0,
>>>    ntpr=5000, ntwx=5000,
>>>    ntt=3, gamma_ln=2.0, ig=676075,
>>>      temp0=298,
>>>   /
>>>
>>>
>>>
>>>
>>> |--------------------- INFORMATION ----------------------
>>> | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
>>> |                      Version 2.1
>>> |
>>> |                      12/20/2010
>>> |
>>> |
>>> | 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:
>>> |      [SPDP] - Hybrid Single/Double Precision (Default).
>>> |
>>> |--------------------------------------------------------
>>>
>>> |------------------- GPU DEVICE INFO --------------------
>>> |
>>> |   CUDA Capable Devices Detected:      1
>>> |           CUDA Device ID in use:      0
>>> |                CUDA Device Name: GeForce GTX 470
>>> |     CUDA Device Global Mem Size:   1279 MB
>>> | CUDA Device Num Multiprocessors:     14
>>> |           CUDA Device Core Freq:   1.22 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 =    43.365
>>>
>>> | New format PARM file being parsed.
>>> | Version =    1.000 Date = 01/21/11 Time = 18:45:59
>>>
>>> | 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  =   92246 NTYPES =      16 NBONH =   89280 MBONA  =    2945
>>>   NTHETH =    6302 MTHETA =    4240 NPHIH =   11120 MPHIA  =    8029
>>>   NHPARM =       0 NPARM  =       0 NNB   =  147846 NRES   =   29261
>>>   NBONA  =    2945 NTHETA =    4240 NPHIA =    8029 NUMBND =      33
>>>   NUMANG =      67 NPTRA  =      38 NATYP =      25 NPHB   =       1
>>>   IFBOX  =       2 NMXRS  =      77 IFCAP =       0 NEXTRA =       0
>>>   NCOPY  =       0
>>>
>>> | Coordinate Index Table dimensions:    17   17   17
>>> | Direct force subcell size =     6.2484    6.2484    6.2484
>>>
>>>       BOX TYPE: TRUNCATED OCTAHEDRON
>>>
>>>
>> ----------------------------------------------------------------------------
>> ----
>>>     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    =    5000, ntrx    =       1, ntwr
>>> =     500
>>>       iwrap   =       0, ntwx    =    5000, ntwv    =       0, ntwe
>>> =       0
>>>       ioutfm  =       0, ntwprt  =       0, idecomp =       0,
>>> rbornstat=      0
>>>
>>> Potential function:
>>>       ntf     =       2, ntb     =       2, 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  =    250000, nscm    =      1000, nrespa  =         1
>>>       t       =   0.00000, dt      =   0.00200, vlimit  =  -1.00000
>>>
>>> Langevin dynamics temperature regulation:
>>>       ig      =  676075
>>>       temp0   = 298.00000, tempi   =   0.00000, gamma_ln=   2.00000
>>>
>>> Pressure regulation:
>>>       ntp     =       1
>>>       pres0   =   1.00000, comp    =  44.60000, taup    =   1.00000
>>>
>>> SHAKE:
>>>       ntc     =       2, jfastw  =       0
>>>       tol     =   0.00001
>>>
>>> | Intermolecular bonds treatment:
>>> |     no_intermolecular_bonds =       1
>>>
>>> | Energy averages sample interval:
>>> |     ene_avg_sampling =    5000
>>>
>>> Ewald parameters:
>>>       verbose =       0, ew_type =       0, nbflag  =       1, use_pme
>>> =       1
>>>       vdwmeth =       1, eedmeth =       1, netfrc  =       1
>>>       Box X =  106.223   Box Y =  106.223   Box Z =  106.223
>>>       Alpha =  109.471   Beta  =  109.471   Gamma =  109.471
>>>       NFFT1 =  108       NFFT2 =  108       NFFT3 =  108
>>>       Cutoff=   10.000   Tol   =0.100E-04
>>>       Ewald Coefficient =  0.27511
>>>       Interpolation order =    4
>>>
>>>
>> ----------------------------------------------------------------------------
>> ----
>>>     3.  ATOMIC COORDINATES AND VELOCITIES
>>>
>> ----------------------------------------------------------------------------
>> ----
>>>
>>>
>>>   begin time read from input coords =  3700.000 ps
>>>
>>>
>>>   Number of triangulated 3-point waters found:    28820
>>>
>>>       Sum of charges from parm topology file =  -0.00266701
>>>       Forcing neutrality...
>>>
>>> | Dynamic Memory, Types Used:
>>> | Reals             2846082
>>> | Integers          2613755
>>>
>>> | Nonbonded Pairs Initial Allocation:    27902108
>>>
>>> | GPU memory information:
>>> | KB of GPU memory in use:    876823
>>> | KB of CPU memory in use:     77099
>>>
>>>
>> ----------------------------------------------------------------------------
>> ----
>>>     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 =     5000   TIME(PS) =    3710.000  TEMP(K) =   298.54  PRESS =
>>> 19.7
>>>   Etot   =   -208138.5945  EKtot   =     55606.0703  EPtot      =
>>> -263744.6648
>>>   BOND   =     12770.3337  ANGLE   =      5327.0090  DIHED      =
>>> 1796.1712
>>>   1-4 NB =      1220.6297  1-4 EEL =     32614.9838  VDWAALS    =
>>> 44968.0029
>>>   EELEC  =   -362441.7951  EHBOND  =         0.0000  RESTRAINT  =
>>> 0.0000
>>>   EKCMT  =     25890.2734  VIRIAL  =     25498.7611  VOLUME     =
>>> 920970.7237
>>>                                                      Density    =
>>> 1.0185
>>>
>> ----------------------------------------------------------------------------
>> --
>>>
>>>
>>>   NSTEP =    10000   TIME(PS) =    3720.000  TEMP(K) =   296.22  PRESS =
>>> 73.8
>>>   Etot   =   -208072.6867  EKtot   =     55172.7422  EPtot      =
>>> -263245.4289
>>>   BOND   =     12797.2804  ANGLE   =      5280.3633  DIHED      =
>>> 1793.7009
>>>   1-4 NB =      1236.9252  1-4 EEL =     32530.0890  VDWAALS    =
>>> 45147.6190
>>>   EELEC  =   -362031.4066  EHBOND  =         0.0000  RESTRAINT  =
>>> 0.0000
>>>   EKCMT  =     25827.2976  VIRIAL  =     24357.5606  VOLUME     =
>>> 921836.9062
>>>                                                      Density    =
>>> 1.0176
>>>
>> ----------------------------------------------------------------------------
>> --
>>>
>>>
>>>   NSTEP =    15000   TIME(PS) =    3730.000  TEMP(K) =   299.32  PRESS =
>>> 133.8
>>>   Etot   =   -207140.0864  EKtot   =     55750.0508  EPtot      =
>>> -262890.1372
>>>   BOND   =     12813.3463  ANGLE   =      5316.1231  DIHED      =
>>> 1777.2270
>>>   1-4 NB =      1214.8564  1-4 EEL =     32504.7227  VDWAALS    =
>>> 45134.9078
>>>   EELEC  =   -361651.3206  EHBOND  =         0.0000  RESTRAINT  =
>>> 0.0000
>>>   EKCMT  =     26061.3868  VIRIAL  =     23397.2429  VOLUME     =
>>> 922304.1794
>>>                                                      Density    =
>>> 1.0171
>>>
>> ----------------------------------------------------------------------------
>> --
>>>
>>>
>>>   NSTEP =    20000   TIME(PS) =    3740.000  TEMP(K) =      NaN  PRESS
>>> =     NaN
>>>   Etot   =            NaN  EKtot   =            NaN  EPtot
>>> =            NaN
>>>   BOND   =         0.0000  ANGLE   =    795708.3759  DIHED      =
>>> 0.0000
>>>   1-4 NB =         0.0000  1-4 EEL =         0.0000  VDWAALS    =
>>> -1408.8764
>>>   EELEC  =            NaN  EHBOND  =         0.0000  RESTRAINT  =
>>> 0.0000
>>>   EKCMT  =         0.0000  VIRIAL  =            NaN  VOLUME
>>> =            NaN
>>>                                                      Density
>>> =            NaN
>>>
>> ----------------------------------------------------------------------------
>> --
>>>
>>>
>>>   NSTEP =    25000   TIME(PS) =    3750.000  TEMP(K) =      NaN  PRESS
>>> =     NaN
>>>   Etot   =            NaN  EKtot   =            NaN  EPtot
>>> =            NaN
>>>   BOND   =         0.0000  ANGLE   =    795708.3759  DIHED      =
>>> 0.0000
>>>   1-4 NB =         0.0000  1-4 EEL =         0.0000  VDWAALS    =
>>> -1408.8764
>>>   EELEC  =            NaN  EHBOND  =         0.0000  RESTRAINT  =
>>> 0.0000
>>>   EKCMT  =         0.0000  VIRIAL  =            NaN  VOLUME
>>> =            NaN
>>>                                                      Density
>>> =            NaN
>>>
>> ----------------------------------------------------------------------------
>> --
>>>
>>>
>>>
>>>
>>>
>>>
>>> Dne Wed, 26 Jan 2011 15:04:16 +0100 case <case.biomaps.rutgers.edu>
>>> napsal/-a:
>>>
>>> > On Wed, Jan 26, 2011, Marek Maly wrote:
>>> >>
>>> >> I recently also obtained  NaN problem in one of my simulation using
>>> >> pmemd.cuda on GTX 470:
>>> >> see - relevant data below. Unfortunately it is unreproducable as I am
>>> >> using ig=-1.
>>> >
>>> > You *can* re-run things in this circumstance: pmemd will print out the
>>> > value
>>> > of the random seed that was actually used, and you can put that back
>> into
>>> > your input file.  This can be helpful to see if the problem is the
>>> same
>>> > every
>>> > time.
>>> >
>>> > ....dac
>>> >
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >
>>> > __________ Informace od ESET NOD32 Antivirus, verze databaze 5820
>>> > (20110126) __________
>>> >
>>> > Tuto zpravu proveril ESET NOD32 Antivirus.
>>> >
>>> > http://www.eset.cz
>>> >
>>> >
>>> >
>>>
>>>
>>> --
>>> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
>>> http://www.opera.com/mail/
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> __________ Informace od ESET NOD32 Antivirus, verze databaze 5821
>> (20110126) __________
>>
>> Tuto zpravu proveril ESET NOD32 Antivirus.
>>
>> http://www.eset.cz
>>
>>
>>
>
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

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Received on Thu Jan 27 2011 - 07:30:03 PST
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