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/
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Received on Wed Jan 26 2011 - 09:00:05 PST
