Ah, so you did. You clearly wrote CPUs, but I was seeing GPUs.
2011/1/26 Marek Maly <marek.maly.ujep.cz>
> No, as I wrote in my last response I am going to do this test right now.
>
> Best,
>
> Marek
>
> Dne Wed, 26 Jan 2011 17:37:49 +0100 Jason Swails <jason.swails.gmail.com>
> napsal/-a:
>
> > One other comment -- to make sure that this is specific GPU issues, have
> > you
> > tried running the same restart simulation using just pmemd (with no GPU)
> > and
> > show that it is in fact a GPU issue?
> >
> > 2011/1/26 Jason Swails <jason.swails.gmail.com>
> >
> >> Hello,
> >>
> >> You really should apply bugfix.12 to compare apples to apples. Another
> >> comment -- the default cut value is 8, not 10, and without bugfix.12 it
> >> was
> >> cut != 8 that caused problems.
> >>
> >> However, bugfix.12 fixed more issues than just cut != 8 (it also fixed
> >> issues with GTX 4xx/5xx.
> >>
> >> Hope this helps,
> >> Jason
> >>
> >> 2011/1/26 Marek Maly <marek.maly.ujep.cz>
> >>
> >> 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
> >>>
> >>
> >>
> >>
> >> --
> >> Jason M. Swails
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Graduate Student
> >> 352-392-4032
> >>
> >
> >
> >
>
>
> --
> 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 26 2011 - 10:30:02 PST
