Hi Ross,
here are the required input data:
http://physics.ujep.cz/~mmaly/Amber/
all the requested information I will send as soon I collect them :))
Pls, let me know if you succeed to reproduce the NaN error
on your GPU system.
Best,
Marek
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
Received on Wed Jan 26 2011 - 10:00:06 PST
