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---- > 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/amberReceived on Wed Jan 26 2011 - 09:00:04 PST