Hi Peker,
first of all, thanks a lot that you will try verify reproducibility
of my version NaN error using my input files ! You have different gcc
version and also GTX 480 instead of GTX 470 but in spite of this
differences it might be interesting and tell us little more.
BTW you have the same gcc and OS (at least the type - UBUNTU) as I have
on our tesla system where I was not able to reproduce this err. so let.s
see.
Anyway my and yours NaN err has the same behaviour. It is not true that in
my case
it immediately interupt the simulation. I just posted starting part of my
OUT file
in my previous email/s. See below the full OUT file from my original run
where I discovered
this err. In the agreement with you I have obtained RST full of NaNs at
the end of the
run so that the consequent part of simulation didn.t start.
Best,
Marek
-------------------------------------------------------
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
------------------------------------------------------------------------------
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
------------------------------------------------------------------------------
NSTEP = 35000 TIME(PS) = 3770.000 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 = 40000 TIME(PS) = 3780.000 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 = 45000 TIME(PS) = 3790.000 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 = 50000 TIME(PS) = 3800.000 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 = 55000 TIME(PS) = 3810.000 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 = 60000 TIME(PS) = 3820.000 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 = 65000 TIME(PS) = 3830.000 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 = 70000 TIME(PS) = 3840.000 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 = 75000 TIME(PS) = 3850.000 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 = 80000 TIME(PS) = 3860.000 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 = 85000 TIME(PS) = 3870.000 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 = 90000 TIME(PS) = 3880.000 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 = 95000 TIME(PS) = 3890.000 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 = 100000 TIME(PS) = 3900.000 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 = 105000 TIME(PS) = 3910.000 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 = 110000 TIME(PS) = 3920.000 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 = 115000 TIME(PS) = 3930.000 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 = 120000 TIME(PS) = 3940.000 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 = 125000 TIME(PS) = 3950.000 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 = 130000 TIME(PS) = 3960.000 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 = 135000 TIME(PS) = 3970.000 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 = 140000 TIME(PS) = 3980.000 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 = 145000 TIME(PS) = 3990.000 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 = 150000 TIME(PS) = 4000.000 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 = 155000 TIME(PS) = 4010.000 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 = 160000 TIME(PS) = 4020.000 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 = 165000 TIME(PS) = 4030.000 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 = 170000 TIME(PS) = 4040.000 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 = 175000 TIME(PS) = 4050.000 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 = 180000 TIME(PS) = 4060.000 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 = 185000 TIME(PS) = 4070.000 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 = 190000 TIME(PS) = 4080.000 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 = 195000 TIME(PS) = 4090.000 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 = 200000 TIME(PS) = 4100.000 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 = 205000 TIME(PS) = 4110.000 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 = 210000 TIME(PS) = 4120.000 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 = 215000 TIME(PS) = 4130.000 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 = 220000 TIME(PS) = 4140.000 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 = 225000 TIME(PS) = 4150.000 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 = 230000 TIME(PS) = 4160.000 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 = 235000 TIME(PS) = 4170.000 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 = 240000 TIME(PS) = 4180.000 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 = 245000 TIME(PS) = 4190.000 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 = 250000 TIME(PS) = 4200.000 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
------------------------------------------------------------------------------
A V E R A G E S O V E R 50 S T E P S
NSTEP = 250000 TIME(PS) = 4200.000 TEMP(K) = NaN PRESS
= NaN
Etot = NaN EKtot = NaN EPtot
= NaN
BOND = 767.6192 ANGLE = 748284.3432 DIHED =
107.3420
1-4 NB = 73.4482 1-4 EEL = 1952.9959 VDWAALS =
1380.6668
EELEC = NaN EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 1555.5792 VIRIAL = NaN VOLUME
= NaN
Density
= NaN
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 250000 TIME(PS) = 4200.000 TEMP(K) = NaN PRESS
= NaN
Etot = NaN EKtot = NaN EPtot
= NaN
BOND = 3038.3275 ANGLE = 187709.7290 DIHED =
424.8768
1-4 NB = 290.7255 1-4 EEL = 7730.1891 VDWAALS =
11041.3482
EELEC = NaN EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 6157.2073 VIRIAL = NaN VOLUME
= NaN
Density
= NaN
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| NonSetup CPU Time in Major Routines:
|
| Routine Sec %
| ------------------------------
| Nonbond 6993.59 91.82
| Bond 0.00 0.00
| Angle 0.00 0.00
| Dihedral 0.00 0.00
| Shake 179.59 2.36
| RunMD 443.18 5.82
| Other 0.15 0.00
| ------------------------------
| Total 7616.51
| PME Nonbond Pairlist CPU Time:
|
| Routine Sec %
| ---------------------------------
| Set Up Cit 0.00 0.00
| Build List 0.00 0.00
| ---------------------------------
| Total 0.00 0.00
| PME Direct Force CPU Time:
|
| Routine Sec %
| ---------------------------------
| NonBonded Calc 0.00 0.00
| Exclude Masked 0.00 0.00
| Other 0.10 0.00
| ---------------------------------
| Total 0.10 0.00
| PME Reciprocal Force CPU Time:
|
| Routine Sec %
| ---------------------------------
| 1D bspline 0.00 0.00
| Grid Charges 0.00 0.00
| Scalar Sum 0.00 0.00
| Gradient Sum 0.00 0.00
| FFT 0.00 0.00
| ---------------------------------
| Total 0.00 0.00
| Final Performance Info:
| -----------------------------------------------------
| Average timings for last 0 steps:
| Elapsed(s) = 0.00 Per Step(ms) = +Infinity
| ns/day = 0.00 seconds/ns = +Infinity
|
| Average timings for all steps:
| Elapsed(s) = 8604.63 Per Step(ms) = 34.42
| ns/day = 5.02 seconds/ns = 17209.27
| -----------------------------------------------------
| Setup CPU time: 0.87 seconds
| NonSetup CPU time: 7616.51 seconds
| Total CPU time: 7617.39 seconds 2.12 hours
| Setup wall time: 1 seconds
| NonSetup wall time: 8605 seconds
| Total wall time: 8606 seconds 2.39 hours
Dne Thu, 27 Jan 2011 01:06:08 +0100 peker milas <pekermilas.gmail.com>
napsal/-a:
> Hi Marek,
>
> Of course i can gladly do that. Probably tomorrow i will start it and
> i will let all of you know about it right away.
>
> By the way, my NaN s look like different than yours in couple ways.
> The first difference is in my case simulation continues and when it
> start another 500 ps calculation it writes down to the .out file
> something like, i couldn't read the .rst file etc... Also because this
> is a set of consecutive runs i was dumping the stdout to a .txt file.
> But i didn't see this kind of a warning in this file.
>
> That is why it is freaking me out and i have no idea about how it
> happens.
> Anyway as i said i will let you know about your simulation soon...
>
> best
> peker
>
> 2011/1/26 Marek Maly <marek.maly.ujep.cz>:
>> Hi Peker,
>>
>> First of all this error message which I reported sooner:
>>
>> -----------------------------------
>> Error: unspecified launch failure launching kernel kClearForces
>> cudaFree GpuBuffer::Deallocate failed unspecified launch failure
>> STOP PMEMD Terminated Abnormally!
>> -----------------------------------
>>
>> has nothing common with the "NaN error story" !
>>
>> That err message I have obtained already several time and was written
>> directly into terminal window
>> from which I started the amber calculation. This error immediately
>> finished calculation so you can
>> find OUT file with nice data but interrupted before regular end of the
>> run
>> without any err message
>> on its end.
>>
>> It is also interesting your information that in your case the NaN error
>> is
>> not reproducible however you are using
>> fixed random seed (not the ig=-1). However you use GTX 480 and my
>> version
>> of NaN error was obtained on GTX 470,
>> can you please just for the curiosity try to run the pmemd.cuda
>> simulation
>> on your system using my input files
>> ( http://physics.ujep.cz/~mmaly/Amber/ ) and let us know if you obtained
>> NaN errors or not ? (it should appear from the
>> time step 20 000).
>>
>> Thanks,
>>
>> Marek
>>
>>
>>
>>
>>
>>
>>
>> Dne Thu, 27 Jan 2011 00:32:38 +0100 peker milas <pekermilas.gmail.com>
>> napsal/-a:
>>
>>> Hello all,
>>>
>>> Although I couldn't join this email traffic fast enough, i need to let
>>> you know about my case. But this time i will be more specific (i
>>> hope). I applied all patches in bugfixes and i actually made a clean
>>> (from scratch) installation. My system is Ubuntu 10.04 with kernel
>>> version 2.6.37-9. My gcc version is 4.4.3. Below is my nvcc --version
>>> output
>>>
>>> nvcc: NVIDIA (R) Cuda compiler driver
>>> Copyright (c) 2005-2010 NVIDIA Corporation
>>> Built on Wed_Nov__3_16:16:57_PDT_2010
>>> Cuda compilation tools, release 3.2, V0.2.1221
>>>
>>> Machine has two intel nehalem cpu packs on it. It has 8 physical 16
>>> logical cores. Our graphics card is GTX 480. Its idle state
>>> temperature is 47 C. When it runs it can reach 90 C quickly (less than
>>> a minute). Then it stabilizes itself at this temperature. The actual
>>> simulation consists of many 500 pico second runs. I decided to use
>>> this time scale right after i had this NaN errors in the first time.
>>> My reasoning based on the observation of first set of NaN s in a
>>> longer run. Back in that time fine part of the .rst file was close to
>>> 800 pico seconds. Then this leads me to divide it into 500 pico second
>>> steps. Again for those runs, i am using a cutoff distance 10 A.
>>> iwrap=1 flag/options is included. But, I am not utilizing ig=-1
>>> flag/option. Basically my input file is exactly same with the input
>>> file
>>> in advanced web tutorial for explicit solvent case except this iwrap
>>> option.
>>>
>>> In my case, i can run pmemd.MPI without seen any errors similar to
>>> this NaN issue. I tested it recently, and a sort of long time ago (say
>>> 1-2 mounts). As Marek said ,unfortunately this error comes from
>>> nowhere and at least for me it is not reproducable.
>>>
>>> Meanwhile, what bothering me is not facing with this problem. It is
>>> rather not to be able to see any kind of warnings or a sign of it. In
>>> other words i don't know how to debug it or observing it among system
>>> messages. For example, again in Marek's email he was
>>> showing a notice like below
>>>
>>> -----------------------------------
>>> Error: unspecified launch failure launching kernel kClearForces
>>> cudaFree GpuBuffer::Deallocate failed unspecified launch failure
>>> STOP PMEMD Terminated Abnormally!
>>> -----------------------------------
>>>
>>> I didn't get this error even in .out file. I have no idea how i should
>>> understand this. If anybody wants to take a look at the any of the
>>> resultant files i can gladly send you a link or attach to my email.
>>> Also, if anybody can tell me in which file or among which messages i
>>> should see a notice/warning/error related with this behavior i will be
>>> so happy. Otherwise this problem will stay as a mistery for me, and
>>> this is highly sad.
>>>
>>> thank you million times
>>> all the best
>>> peker
>>>
>>>
>>> 2011/1/26 Jason Swails <jason.swails.gmail.com>:
>>>> 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
>>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> __________ Informace od ESET NOD32 Antivirus, verze databaze 5822
>>> (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 5822
> (20110126) __________
>
> Tuto zpravu proveril ESET NOD32 Antivirus.
>
> http://www.eset.cz
>
>
>
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
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Received on Wed Jan 26 2011 - 16:30:04 PST
