Hi Peker and Ross,
I did also short simulations ( 50 000 x 2fs each ) under all NTT/NTB
combinations suggested by Ross.
In cases where generator of random numbers is required I used always that
problematic seed ( 676075 ) from my original
case. List of all OUT files is below. The only problematic combination
regarding to NaN error is NTT3/NTB2. I have to
repeat again here that regarding to my NaN error also the given seed is
important. As I mentioned sooner I can
"solve" this NaN problem by restarting the "NaN affected" part of
simulation ( having ig=-1 ) so new seed usually
solve the situation.
Regarding to that error which Peker mentioned:
> Error: unspecified launch failure launching kernel kClearForces
> cudaFree GpuBuffer::Deallocate failed unspecified launch failure
I also wrote about it on the start of this discussion. This error from
time to time
interupts the given MD period (without any err message in OUT file). I
have experienced
this err several time almost on all machines in our lab during different
simulations.
We speculated on the start of this discussion that the source might be GPU
overheating
etc ... Someone suggested in this thread to put between each two
consecutive MD runs (let say some hundred thousands steps long) small pause
(if I remember suggested was 10 minutes to allow card cool down).
Best wishes,
Marek
***************** NTT_3-NTB_2 *********************
***************** NTT_3-NTB_2 *********************
***************** NTT_3-NTB_2 *********************
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 11
| Run on 01/28/2011 at 11:05:13
[-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=50000,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 = 50000, 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
------------------------------------------------------------------------------
A V E R A G E S O V E R 10 S T E P S
NSTEP = 50000 TIME(PS) = 3800.000 TEMP(K) = NaN PRESS
= NaN
Etot = NaN EKtot = NaN EPtot
= NaN
BOND = 3838.0960 ANGLE = 558588.2126 DIHED =
536.7099
1-4 NB = 367.2411 1-4 EEL = 9764.9796 VDWAALS =
12538.8395
EELEC = NaN EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 7777.8958 VIRIAL = NaN VOLUME
= NaN
Density
= NaN
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 50000 TIME(PS) = 3800.000 TEMP(K) = NaN PRESS
= NaN
Etot = NaN EKtot = NaN EPtot
= NaN
BOND = 5862.7966 ANGLE = 362207.0324 DIHED =
819.8509
1-4 NB = 560.9934 1-4 EEL = 14916.2750 VDWAALS =
21305.5351
EELEC = NaN EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 11881.0556 VIRIAL = NaN VOLUME
= NaN
Density
= NaN
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| NonSetup CPU Time in Major Routines:
|
| Routine Sec %
| ------------------------------
| Nonbond 1680.59 92.38
| Bond 0.00 0.00
| Angle 0.00 0.00
| Dihedral 0.00 0.00
| Shake 35.83 1.97
| RunMD 102.77 5.65
| Other 0.03 0.00
| ------------------------------
| Total 1819.22
| 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 0.02 0.00
| ---------------------------------
| Total 0.02 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) = 1899.48 Per Step(ms) = 37.99
| ns/day = 4.55 seconds/ns = 18994.82
| -----------------------------------------------------
| Setup CPU time: 1.49 seconds
| NonSetup CPU time: 1819.22 seconds
| Total CPU time: 1820.72 seconds 0.51 hours
| Setup wall time: 3 seconds
| NonSetup wall time: 1899 seconds
| Total wall time: 1902 seconds 0.53 hours
************************************ NTT_3-NTB_1
*************************************************
************************************ NTT_3-NTB_1
*************************************************
************************************ NTT_3-NTB_1
*************************************************
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 11
| Run on 01/29/2011 at 20:16:51
[-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=50000,dt=0.002,
ntc=2,ntf=2,
cut=10.0, ntb=1,
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 = 1, 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 = 50000, 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
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 2453308
| Integers 2463491
| Nonbonded Pairs Initial Allocation: 27902108
| GPU memory information:
| KB of GPU memory in use: 778814
| KB of CPU memory in use: 72099
--------------------------------------------------------------------------------
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) = 299.25 PRESS
= 0.0
Etot = -207384.6850 EKtot = 55738.1211 EPtot =
-263122.8061
BOND = 12840.5650 ANGLE = 5357.9672 DIHED =
1789.1215
1-4 NB = 1238.7644 1-4 EEL = 32514.3390 VDWAALS =
44833.5070
EELEC = -361697.0701 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NSTEP = 10000 TIME(PS) = 3720.000 TEMP(K) = 297.98 PRESS
= 0.0
Etot = -207889.1650 EKtot = 55500.5664 EPtot =
-263389.7314
BOND = 12813.6401 ANGLE = 5290.8917 DIHED =
1768.5496
1-4 NB = 1231.4728 1-4 EEL = 32576.0217 VDWAALS =
45137.4371
EELEC = -362207.7444 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NSTEP = 15000 TIME(PS) = 3730.000 TEMP(K) = 299.25 PRESS
= 0.0
Etot = -207681.9962 EKtot = 55737.7422 EPtot =
-263419.7384
BOND = 12807.6625 ANGLE = 5315.5897 DIHED =
1789.2179
1-4 NB = 1252.1244 1-4 EEL = 32527.9657 VDWAALS =
44805.5642
EELEC = -361917.8629 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NSTEP = 20000 TIME(PS) = 3740.000 TEMP(K) = 299.46 PRESS
= 0.0
Etot = -207942.4617 EKtot = 55777.1914 EPtot =
-263719.6531
BOND = 12835.6876 ANGLE = 5258.8579 DIHED =
1820.8942
1-4 NB = 1251.3720 1-4 EEL = 32559.0879 VDWAALS =
45495.7052
EELEC = -362941.2579 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NSTEP = 25000 TIME(PS) = 3750.000 TEMP(K) = 299.50 PRESS
= 0.0
Etot = -208190.1680 EKtot = 55783.8008 EPtot =
-263973.9688
BOND = 12821.7590 ANGLE = 5382.7608 DIHED =
1799.1085
1-4 NB = 1251.3135 1-4 EEL = 32531.8455 VDWAALS =
45362.8754
EELEC = -363123.6316 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NSTEP = 30000 TIME(PS) = 3760.000 TEMP(K) = 297.84 PRESS
= 0.0
Etot = -207879.6190 EKtot = 55474.8555 EPtot =
-263354.4745
BOND = 12730.7839 ANGLE = 5358.6906 DIHED =
1817.7316
1-4 NB = 1241.1404 1-4 EEL = 32584.1836 VDWAALS =
45582.3899
EELEC = -362669.3945 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NSTEP = 35000 TIME(PS) = 3770.000 TEMP(K) = 298.98 PRESS
= 0.0
Etot = -207376.6019 EKtot = 55686.8555 EPtot =
-263063.4574
BOND = 12876.9217 ANGLE = 5339.1508 DIHED =
1783.4435
1-4 NB = 1255.5544 1-4 EEL = 32602.1902 VDWAALS =
44743.5949
EELEC = -361664.3129 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NSTEP = 40000 TIME(PS) = 3780.000 TEMP(K) = 297.15 PRESS
= 0.0
Etot = -208582.9892 EKtot = 55345.6094 EPtot =
-263928.5985
BOND = 12675.0071 ANGLE = 5291.5926 DIHED =
1790.3650
1-4 NB = 1219.2393 1-4 EEL = 32533.9573 VDWAALS =
44654.1572
EELEC = -362092.9169 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NSTEP = 45000 TIME(PS) = 3790.000 TEMP(K) = 298.79 PRESS
= 0.0
Etot = -207863.4317 EKtot = 55652.5508 EPtot =
-263515.9825
BOND = 12862.8409 ANGLE = 5292.6938 DIHED =
1808.4920
1-4 NB = 1263.0239 1-4 EEL = 32615.6800 VDWAALS =
45221.4712
EELEC = -362580.1844 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NSTEP = 50000 TIME(PS) = 3800.000 TEMP(K) = 297.69 PRESS
= 0.0
Etot = -208031.6964 EKtot = 55447.1250 EPtot =
-263478.8214
BOND = 12899.6401 ANGLE = 5369.3732 DIHED =
1821.0623
1-4 NB = 1221.0008 1-4 EEL = 32509.0325 VDWAALS =
45456.7132
EELEC = -362755.6436 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
A V E R A G E S O V E R 10 S T E P S
NSTEP = 50000 TIME(PS) = 3800.000 TEMP(K) = 298.59 PRESS
= 0.0
Etot = -207882.2814 EKtot = 55614.4418 EPtot =
-263496.7232
BOND = 12816.4508 ANGLE = 5325.7568 DIHED =
1798.7986
1-4 NB = 1242.5006 1-4 EEL = 32555.4303 VDWAALS =
45129.3415
EELEC = -362365.0019 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 50000 TIME(PS) = 3800.000 TEMP(K) = 0.81 PRESS
= 0.0
Etot = 339.9367 EKtot = 150.0277 EPtot =
288.0643
BOND = 64.1399 ANGLE = 39.3804 DIHED =
16.8634
1-4 NB = 14.0760 1-4 EEL = 35.6280 VDWAALS =
328.1294
EELEC = 493.4512 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| NonSetup CPU Time in Major Routines:
|
| Routine Sec %
| ------------------------------
| Nonbond 2062.55 93.32
| Bond 0.00 0.00
| Angle 0.00 0.00
| Dihedral 0.00 0.00
| Shake 35.32 1.60
| RunMD 112.24 5.08
| Other 0.02 0.00
| ------------------------------
| Total 2210.13
| 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 0.01 0.00
| ---------------------------------
| Total 0.01 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) = 2316.08 Per Step(ms) = 46.32
| ns/day = 3.73 seconds/ns = 23160.78
| -----------------------------------------------------
| Setup CPU time: 0.88 seconds
| NonSetup CPU time: 2210.13 seconds
| Total CPU time: 2211.01 seconds 0.61 hours
| Setup wall time: 1 seconds
| NonSetup wall time: 2316 seconds
| Total wall time: 2317 seconds 0.64 hours
************************************ NTT_1-NTB_2
*********************************
************************************ NTT_1-NTB_2
*********************************
************************************ NTT_1-NTB_2
*********************************
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 11
| Run on 01/29/2011 at 21:30:02
[-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=50000,dt=0.002,
ntc=2,ntf=2,
cut=10.0, ntb=2, ntp=1, taup=1.0,
ntpr=5000, ntwx=5000,
ntt=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 = 50000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -1.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 298.00000, tempi = 0.00000, tautp = 1.00000
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: 599159
| KB of CPU memory in use: 76459
--------------------------------------------------------------------------------
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
|---------------------------------------------------
check COM velocity, temp: 0.001323 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000004 0.00(Removed)
check COM velocity, temp: 0.000006 0.00(Removed)
check COM velocity, temp: 0.000005 0.00(Removed)
NSTEP = 5000 TIME(PS) = 3710.000 TEMP(K) = 298.48 PRESS =
-24.0
Etot = -207964.4103 EKtot = 55593.6953 EPtot =
-263558.1056
BOND = 12879.0066 ANGLE = 5206.9284 DIHED =
1778.4333
1-4 NB = 1202.5234 1-4 EEL = 32547.3891 VDWAALS =
45184.3060
EELEC = -362356.6925 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 25823.0630 VIRIAL = 26300.6166 VOLUME =
923120.9461
Density =
1.0162
------------------------------------------------------------------------------
check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000007 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000007 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
NSTEP = 10000 TIME(PS) = 3720.000 TEMP(K) = 297.13 PRESS =
58.8
Etot = -207947.4615 EKtot = 55342.4492 EPtot =
-263289.9107
BOND = 12760.2267 ANGLE = 5221.8221 DIHED =
1795.9887
1-4 NB = 1258.6231 1-4 EEL = 32570.9474 VDWAALS =
45045.8676
EELEC = -361943.3864 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 25864.0785 VIRIAL = 24693.0184 VOLUME =
922328.9992
Density =
1.0170
------------------------------------------------------------------------------
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000005 0.00(Removed)
check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000007 0.00(Removed)
NSTEP = 15000 TIME(PS) = 3730.000 TEMP(K) = 297.29 PRESS
= 1.3
Etot = -207962.6017 EKtot = 55371.2383 EPtot =
-263333.8400
BOND = 12883.1536 ANGLE = 5223.9966 DIHED =
1764.8867
1-4 NB = 1229.6042 1-4 EEL = 32629.8483 VDWAALS =
44711.8286
EELEC = -361777.1580 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 25671.6327 VIRIAL = 25645.4435 VOLUME =
921052.6580
Density =
1.0185
------------------------------------------------------------------------------
check COM velocity, temp: 0.000007 0.00(Removed)
check COM velocity, temp: 0.000007 0.00(Removed)
check COM velocity, temp: 0.000008 0.00(Removed)
check COM velocity, temp: 0.000005 0.00(Removed)
check COM velocity, temp: 0.000005 0.00(Removed)
NSTEP = 20000 TIME(PS) = 3740.000 TEMP(K) = 298.51 PRESS =
-25.3
Etot = -207798.6788 EKtot = 55599.6289 EPtot =
-263398.3077
BOND = 12640.9738 ANGLE = 5214.1430 DIHED =
1806.1391
1-4 NB = 1222.5342 1-4 EEL = 32558.9369 VDWAALS =
45163.2769
EELEC = -362004.3117 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 26115.2776 VIRIAL = 26620.0930 VOLUME =
923228.7937
Density =
1.0161
------------------------------------------------------------------------------
check COM velocity, temp: 0.000005 0.00(Removed)
check COM velocity, temp: 0.000005 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000008 0.00(Removed)
NSTEP = 25000 TIME(PS) = 3750.000 TEMP(K) = 296.96 PRESS =
43.9
Etot = -207868.8143 EKtot = 55309.7891 EPtot =
-263178.6034
BOND = 12796.8428 ANGLE = 5269.8050 DIHED =
1785.1785
1-4 NB = 1220.7849 1-4 EEL = 32533.5400 VDWAALS =
45015.1537
EELEC = -361799.9082 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 25833.8367 VIRIAL = 24960.5383 VOLUME =
922015.5062
Density =
1.0174
------------------------------------------------------------------------------
check COM velocity, temp: 0.000005 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000008 0.00(Removed)
check COM velocity, temp: 0.000005 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
NSTEP = 30000 TIME(PS) = 3760.000 TEMP(K) = 297.95 PRESS =
-16.3
Etot = -207852.3766 EKtot = 55494.1758 EPtot =
-263346.5524
BOND = 12626.8247 ANGLE = 5226.2217 DIHED =
1787.5919
1-4 NB = 1258.8821 1-4 EEL = 32675.2034 VDWAALS =
45160.3228
EELEC = -362081.5990 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 26080.4748 VIRIAL = 26405.6889 VOLUME =
923859.1695
Density =
1.0154
------------------------------------------------------------------------------
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000005 0.00(Removed)
check COM velocity, temp: 0.000009 0.00(Removed)
NSTEP = 35000 TIME(PS) = 3770.000 TEMP(K) = 297.77 PRESS =
-59.0
Etot = -207822.2228 EKtot = 55461.6914 EPtot =
-263283.9142
BOND = 12757.7359 ANGLE = 5232.3631 DIHED =
1773.5113
1-4 NB = 1244.5658 1-4 EEL = 32599.1970 VDWAALS =
44518.4133
EELEC = -361409.7006 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 26043.0805 VIRIAL = 27218.9508 VOLUME =
922455.2522
Density =
1.0169
------------------------------------------------------------------------------
check COM velocity, temp: 0.000008 0.00(Removed)
check COM velocity, temp: 0.000005 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000004 0.00(Removed)
check COM velocity, temp: 0.000010 0.00(Removed)
NSTEP = 40000 TIME(PS) = 3780.000 TEMP(K) = 297.15 PRESS =
-53.1
Etot = -207858.4473 EKtot = 55345.0117 EPtot =
-263203.4590
BOND = 12862.2306 ANGLE = 5228.6187 DIHED =
1787.9875
1-4 NB = 1231.9760 1-4 EEL = 32527.4787 VDWAALS =
44957.6127
EELEC = -361799.3632 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 25811.2888 VIRIAL = 26869.9738 VOLUME =
922807.5729
Density =
1.0165
------------------------------------------------------------------------------
check COM velocity, temp: 0.000004 0.00(Removed)
check COM velocity, temp: 0.000010 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000008 0.00(Removed)
NSTEP = 45000 TIME(PS) = 3790.000 TEMP(K) = 298.54 PRESS =
-32.2
Etot = -207937.9036 EKtot = 55603.5469 EPtot =
-263541.4505
BOND = 12612.6844 ANGLE = 5290.3547 DIHED =
1822.2844
1-4 NB = 1260.5899 1-4 EEL = 32598.2038 VDWAALS =
44815.5038
EELEC = -361941.0715 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 25943.3679 VIRIAL = 26584.5052 VOLUME =
923392.2906
Density =
1.0159
------------------------------------------------------------------------------
check COM velocity, temp: 0.000001 0.00(Removed)
check COM velocity, temp: 0.000004 0.00(Removed)
check COM velocity, temp: 0.000008 0.00(Removed)
check COM velocity, temp: 0.000007 0.00(Removed)
check COM velocity, temp: 0.000005 0.00(Removed)
NSTEP = 50000 TIME(PS) = 3800.000 TEMP(K) = 297.71 PRESS =
29.4
Etot = -207973.8795 EKtot = 55450.7344 EPtot =
-263424.6139
BOND = 12966.6408 ANGLE = 5184.0635 DIHED =
1805.1636
1-4 NB = 1201.1537 1-4 EEL = 32443.6326 VDWAALS =
45009.6845
EELEC = -362034.9527 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 26006.8688 VIRIAL = 25420.5772 VOLUME =
922947.7556
Density =
1.0164
------------------------------------------------------------------------------
A V E R A G E S O V E R 10 S T E P S
NSTEP = 50000 TIME(PS) = 3800.000 TEMP(K) = 297.75 PRESS =
-7.7
Etot = -207898.6796 EKtot = 55457.1961 EPtot =
-263355.8757
BOND = 12778.6320 ANGLE = 5229.8317 DIHED =
1790.7165
1-4 NB = 1233.1237 1-4 EEL = 32568.4377 VDWAALS =
44958.1970
EELEC = -361914.8144 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 25919.2969 VIRIAL = 26071.9406 VOLUME =
922720.8944
Density =
1.0166
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 50000 TIME(PS) = 3800.000 TEMP(K) = 0.58 PRESS =
38.1
Etot = 62.0324 EKtot = 107.9986 EPtot =
121.0863
BOND = 115.7483 ANGLE = 28.7149 DIHED =
16.2261
1-4 NB = 21.0608 1-4 EEL = 60.0114 VDWAALS =
205.4478
EELEC = 234.0179 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 134.3779 VIRIAL = 801.3850 VOLUME =
756.8460
Density =
0.0008
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| NonSetup CPU Time in Major Routines:
|
| Routine Sec %
| ------------------------------
| Nonbond 2329.45 94.23
| Bond 0.00 0.00
| Angle 0.00 0.00
| Dihedral 0.00 0.00
| Shake 35.23 1.43
| RunMD 107.26 4.34
| Other 0.03 0.00
| ------------------------------
| Total 2471.97
| 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 0.02 0.00
| ---------------------------------
| Total 0.02 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) = 2598.16 Per Step(ms) = 51.96
| ns/day = 3.33 seconds/ns = 25981.63
| -----------------------------------------------------
| Setup CPU time: 0.77 seconds
| NonSetup CPU time: 2471.97 seconds
| Total CPU time: 2472.74 seconds 0.69 hours
| Setup wall time: 1 seconds
| NonSetup wall time: 2598 seconds
| Total wall time: 2599 seconds 0.72 hours
********************************************* NTT_1-NTB_1
***************************************
********************************************* NTT_1-NTB_1
***************************************
********************************************* NTT_1-NTB_1
***************************************
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 11
| Run on 01/30/2011 at 00:44:23
[-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=50000,dt=0.002,
ntc=2,ntf=2,
cut=10.0, ntb=1,
ntpr=5000, ntwx=5000,
ntt=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 = 1, 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 = 50000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -1.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 298.00000, tempi = 0.00000, tautp = 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 2453308
| Integers 2463491
| Nonbonded Pairs Initial Allocation: 27902108
| GPU memory information:
| KB of GPU memory in use: 501151
| KB of CPU memory in use: 71459
--------------------------------------------------------------------------------
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
|---------------------------------------------------
check COM velocity, temp: 0.001322 0.00(Removed)
check COM velocity, temp: 0.000008 0.00(Removed)
check COM velocity, temp: 0.000008 0.00(Removed)
check COM velocity, temp: 0.000005 0.00(Removed)
check COM velocity, temp: 0.000013 0.00(Removed)
NSTEP = 5000 TIME(PS) = 3710.000 TEMP(K) = 299.64 PRESS
= 0.0
Etot = -207922.8648 EKtot = 55808.5430 EPtot =
-263731.4078
BOND = 12992.8231 ANGLE = 5302.3173 DIHED =
1777.1243
1-4 NB = 1221.3311 1-4 EEL = 32596.8554 VDWAALS =
45248.8311
EELEC = -362870.6901 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
check COM velocity, temp: 0.000004 0.00(Removed)
check COM velocity, temp: 0.000006 0.00(Removed)
check COM velocity, temp: 0.000006 0.00(Removed)
check COM velocity, temp: 0.000004 0.00(Removed)
check COM velocity, temp: 0.000007 0.00(Removed)
NSTEP = 10000 TIME(PS) = 3720.000 TEMP(K) = 297.05 PRESS
= 0.0
Etot = -207863.8952 EKtot = 55327.5117 EPtot =
-263191.4069
BOND = 12721.7604 ANGLE = 5333.9682 DIHED =
1814.9534
1-4 NB = 1251.1871 1-4 EEL = 32532.4639 VDWAALS =
44816.4352
EELEC = -361662.1752 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
check COM velocity, temp: 0.000006 0.00(Removed)
check COM velocity, temp: 0.000008 0.00(Removed)
check COM velocity, temp: 0.000009 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000004 0.00(Removed)
NSTEP = 15000 TIME(PS) = 3730.000 TEMP(K) = 297.80 PRESS
= 0.0
Etot = -207744.4892 EKtot = 55467.4609 EPtot =
-263211.9501
BOND = 12738.9516 ANGLE = 5269.2234 DIHED =
1824.2187
1-4 NB = 1248.0358 1-4 EEL = 32559.6214 VDWAALS =
44814.3743
EELEC = -361666.3753 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
check COM velocity, temp: 0.000004 0.00(Removed)
check COM velocity, temp: 0.000009 0.00(Removed)
check COM velocity, temp: 0.000010 0.00(Removed)
check COM velocity, temp: 0.000006 0.00(Removed)
check COM velocity, temp: 0.000001 0.00(Removed)
NSTEP = 20000 TIME(PS) = 3740.000 TEMP(K) = 298.69 PRESS
= 0.0
Etot = -207871.7363 EKtot = 55632.0391 EPtot =
-263503.7753
BOND = 12750.2116 ANGLE = 5335.8169 DIHED =
1811.5783
1-4 NB = 1214.8507 1-4 EEL = 32573.0376 VDWAALS =
44898.8816
EELEC = -362088.1522 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000005 0.00(Removed)
check COM velocity, temp: 0.000009 0.00(Removed)
check COM velocity, temp: 0.000004 0.00(Removed)
check COM velocity, temp: 0.000004 0.00(Removed)
NSTEP = 25000 TIME(PS) = 3750.000 TEMP(K) = 297.15 PRESS
= 0.0
Etot = -207790.2835 EKtot = 55345.0664 EPtot =
-263135.3499
BOND = 12737.6878 ANGLE = 5317.1513 DIHED =
1787.0285
1-4 NB = 1214.5733 1-4 EEL = 32508.9722 VDWAALS =
44998.4914
EELEC = -361699.2544 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
check COM velocity, temp: 0.000001 0.00(Removed)
check COM velocity, temp: 0.000007 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000006 0.00(Removed)
check COM velocity, temp: 0.000004 0.00(Removed)
NSTEP = 30000 TIME(PS) = 3760.000 TEMP(K) = 297.66 PRESS
= 0.0
Etot = -207821.6469 EKtot = 55440.8750 EPtot =
-263262.5219
BOND = 12839.7999 ANGLE = 5217.1581 DIHED =
1798.8082
1-4 NB = 1208.6666 1-4 EEL = 32492.0695 VDWAALS =
44726.6494
EELEC = -361545.6736 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000004 0.00(Removed)
check COM velocity, temp: 0.000005 0.00(Removed)
check COM velocity, temp: 0.000004 0.00(Removed)
NSTEP = 35000 TIME(PS) = 3770.000 TEMP(K) = 297.42 PRESS
= 0.0
Etot = -207959.2143 EKtot = 55395.1016 EPtot =
-263354.3158
BOND = 12751.3587 ANGLE = 5241.3667 DIHED =
1812.9659
1-4 NB = 1224.4546 1-4 EEL = 32530.4384 VDWAALS =
45032.8291
EELEC = -361947.7291 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000005 0.00(Removed)
check COM velocity, temp: 0.000004 0.00(Removed)
check COM velocity, temp: 0.000008 0.00(Removed)
check COM velocity, temp: 0.000007 0.00(Removed)
NSTEP = 40000 TIME(PS) = 3780.000 TEMP(K) = 297.78 PRESS
= 0.0
Etot = -207898.0235 EKtot = 55462.2031 EPtot =
-263360.2267
BOND = 12718.1123 ANGLE = 5338.4076 DIHED =
1812.2274
1-4 NB = 1204.5141 1-4 EEL = 32615.3949 VDWAALS =
45516.7122
EELEC = -362565.5951 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000001 0.00(Removed)
check COM velocity, temp: 0.000001 0.00(Removed)
check COM velocity, temp: 0.000010 0.00(Removed)
check COM velocity, temp: 0.000001 0.00(Removed)
NSTEP = 45000 TIME(PS) = 3790.000 TEMP(K) = 296.05 PRESS
= 0.0
Etot = -207837.6068 EKtot = 55140.6484 EPtot =
-262978.2552
BOND = 12782.0078 ANGLE = 5268.6883 DIHED =
1833.4654
1-4 NB = 1215.5825 1-4 EEL = 32576.6937 VDWAALS =
44829.7819
EELEC = -361484.4749 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
check COM velocity, temp: 0.000007 0.00(Removed)
check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000004 0.00(Removed)
check COM velocity, temp: 0.000004 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
NSTEP = 50000 TIME(PS) = 3800.000 TEMP(K) = 297.77 PRESS
= 0.0
Etot = -207738.1355 EKtot = 55461.2852 EPtot =
-263199.4207
BOND = 12846.2953 ANGLE = 5201.5101 DIHED =
1783.4057
1-4 NB = 1206.0550 1-4 EEL = 32565.8929 VDWAALS =
44888.7358
EELEC = -361691.3154 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
A V E R A G E S O V E R 10 S T E P S
NSTEP = 50000 TIME(PS) = 3800.000 TEMP(K) = 297.70 PRESS
= 0.0
Etot = -207844.7896 EKtot = 55448.0734 EPtot =
-263292.8630
BOND = 12787.9008 ANGLE = 5282.5608 DIHED =
1805.5776
1-4 NB = 1220.9251 1-4 EEL = 32555.1440 VDWAALS =
44977.1722
EELEC = -361922.1435 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 50000 TIME(PS) = 3800.000 TEMP(K) = 0.91 PRESS
= 0.0
Etot = 69.3593 EKtot = 169.4241 EPtot =
198.8468
BOND = 80.6532 ANGLE = 48.0610 DIHED =
17.4328
1-4 NB = 15.5239 1-4 EEL = 36.7766 VDWAALS =
227.8661
EELEC = 437.1761 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| NonSetup CPU Time in Major Routines:
|
| Routine Sec %
| ------------------------------
| Nonbond 2059.97 94.67
| Bond 0.00 0.00
| Angle 0.00 0.00
| Dihedral 0.00 0.00
| Shake 35.14 1.61
| RunMD 80.88 3.72
| Other 0.03 0.00
| ------------------------------
| Total 2176.03
| 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 0.02 0.00
| ---------------------------------
| Total 0.02 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) = 2270.83 Per Step(ms) = 45.42
| ns/day = 3.80 seconds/ns = 22708.29
| -----------------------------------------------------
| Setup CPU time: 0.82 seconds
| NonSetup CPU time: 2176.03 seconds
| Total CPU time: 2176.84 seconds 0.60 hours
| Setup wall time: 1 seconds
| NonSetup wall time: 2271 seconds
| Total wall time: 2272 seconds 0.63 hours
******************************************** NTT_0-NTB_1
************************************
******************************************** NTT_0-NTB_1
************************************
******************************************** NTT_0-NTB_1
************************************
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 11
| Run on 01/30/2011 at 02:03:13
[-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=50000,dt=0.002,
ntc=2,ntf=2,
cut=10.0, ntb=1,
ntpr=5000, ntwx=5000,
ntt=0,
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 = 1, 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 = 50000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -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 2453308
| Integers 2463491
| Nonbonded Pairs Initial Allocation: 27902108
| GPU memory information:
| KB of GPU memory in use: 501151
| KB of CPU memory in use: 71459
--------------------------------------------------------------------------------
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
|---------------------------------------------------
check COM velocity, temp: 0.001324 0.00(Removed)
check COM velocity, temp: 0.000004 0.00(Removed)
check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000001 0.00(Removed)
check COM velocity, temp: 0.000002 0.00(Removed)
NSTEP = 5000 TIME(PS) = 3710.000 TEMP(K) = 298.83 PRESS
= 0.0
Etot = -207453.3175 EKtot = 55657.9766 EPtot =
-263111.2940
BOND = 12750.6097 ANGLE = 5331.7391 DIHED =
1807.0948
1-4 NB = 1229.5301 1-4 EEL = 32474.7068 VDWAALS =
44494.1174
EELEC = -361199.0919 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
check COM velocity, temp: 0.000001 0.00(Removed)
check COM velocity, temp: 0.000004 0.00(Removed)
check COM velocity, temp: 0.000004 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000001 0.00(Removed)
NSTEP = 10000 TIME(PS) = 3720.000 TEMP(K) = 299.15 PRESS
= 0.0
Etot = -207453.8206 EKtot = 55718.6289 EPtot =
-263172.4495
BOND = 12800.0205 ANGLE = 5278.1236 DIHED =
1774.4143
1-4 NB = 1233.2350 1-4 EEL = 32582.3544 VDWAALS =
44681.3358
EELEC = -361521.9331 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
check COM velocity, temp: 0.000007 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000005 0.00(Removed)
check COM velocity, temp: 0.000004 0.00(Removed)
check COM velocity, temp: 0.000002 0.00(Removed)
NSTEP = 15000 TIME(PS) = 3730.000 TEMP(K) = 298.34 PRESS
= 0.0
Etot = -207454.3113 EKtot = 55567.7891 EPtot =
-263022.1003
BOND = 12861.4404 ANGLE = 5299.7587 DIHED =
1779.6303
1-4 NB = 1223.3422 1-4 EEL = 32479.2893 VDWAALS =
44957.5476
EELEC = -361623.1089 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
check COM velocity, temp: 0.000005 0.00(Removed)
check COM velocity, temp: 0.000005 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000007 0.00(Removed)
NSTEP = 20000 TIME(PS) = 3740.000 TEMP(K) = 298.61 PRESS
= 0.0
Etot = -207453.2234 EKtot = 55616.9023 EPtot =
-263070.1258
BOND = 12722.8661 ANGLE = 5348.1175 DIHED =
1800.7182
1-4 NB = 1219.5729 1-4 EEL = 32482.2948 VDWAALS =
44812.5558
EELEC = -361456.2510 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000005 0.00(Removed)
check COM velocity, temp: 0.000008 0.00(Removed)
check COM velocity, temp: 0.000010 0.00(Removed)
check COM velocity, temp: 0.000009 0.00(Removed)
NSTEP = 25000 TIME(PS) = 3750.000 TEMP(K) = 298.93 PRESS
= 0.0
Etot = -207454.8278 EKtot = 55677.7930 EPtot =
-263132.6208
BOND = 12772.7124 ANGLE = 5189.7392 DIHED =
1804.1016
1-4 NB = 1243.1889 1-4 EEL = 32560.1409 VDWAALS =
44979.9643
EELEC = -361682.4681 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
check COM velocity, temp: 0.000007 0.00(Removed)
check COM velocity, temp: 0.000007 0.00(Removed)
check COM velocity, temp: 0.000008 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
NSTEP = 30000 TIME(PS) = 3760.000 TEMP(K) = 298.98 PRESS
= 0.0
Etot = -207453.6179 EKtot = 55685.9531 EPtot =
-263139.5710
BOND = 12802.5224 ANGLE = 5265.9605 DIHED =
1778.5070
1-4 NB = 1240.2126 1-4 EEL = 32634.3461 VDWAALS =
45159.7019
EELEC = -362020.8216 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000004 0.00(Removed)
check COM velocity, temp: 0.000006 0.00(Removed)
check COM velocity, temp: 0.000007 0.00(Removed)
check COM velocity, temp: 0.000006 0.00(Removed)
NSTEP = 35000 TIME(PS) = 3770.000 TEMP(K) = 299.27 PRESS
= 0.0
Etot = -207454.5056 EKtot = 55740.9063 EPtot =
-263195.4119
BOND = 12749.0275 ANGLE = 5331.7122 DIHED =
1778.1252
1-4 NB = 1242.4994 1-4 EEL = 32664.4998 VDWAALS =
45004.0743
EELEC = -361965.3503 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
check COM velocity, temp: 0.000008 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000005 0.00(Removed)
check COM velocity, temp: 0.000005 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
NSTEP = 40000 TIME(PS) = 3780.000 TEMP(K) = 299.42 PRESS
= 0.0
Etot = -207455.4914 EKtot = 55768.7734 EPtot =
-263224.2648
BOND = 12873.4405 ANGLE = 5237.6511 DIHED =
1800.7664
1-4 NB = 1228.7056 1-4 EEL = 32611.0549 VDWAALS =
45193.5272
EELEC = -362169.4105 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
check COM velocity, temp: 0.000001 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000001 0.00(Removed)
NSTEP = 45000 TIME(PS) = 3790.000 TEMP(K) = 300.69 PRESS
= 0.0
Etot = -207451.1069 EKtot = 56004.9883 EPtot =
-263456.0952
BOND = 12721.1834 ANGLE = 5248.8939 DIHED =
1809.9916
1-4 NB = 1235.1264 1-4 EEL = 32707.3908 VDWAALS =
45358.7267
EELEC = -362537.4080 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000006 0.00(Removed)
check COM velocity, temp: 0.000004 0.00(Removed)
check COM velocity, temp: 0.000006 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
NSTEP = 50000 TIME(PS) = 3800.000 TEMP(K) = 298.88 PRESS
= 0.0
Etot = -207448.8467 EKtot = 55668.0156 EPtot =
-263116.8624
BOND = 12860.9089 ANGLE = 5311.2564 DIHED =
1799.1028
1-4 NB = 1234.2174 1-4 EEL = 32608.5052 VDWAALS =
44343.5380
EELEC = -361274.3911 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
A V E R A G E S O V E R 10 S T E P S
NSTEP = 50000 TIME(PS) = 3800.000 TEMP(K) = 299.11 PRESS
= 0.0
Etot = -207453.3069 EKtot = 55710.7727 EPtot =
-263164.0796
BOND = 12791.4732 ANGLE = 5284.2952 DIHED =
1793.2452
1-4 NB = 1232.9630 1-4 EEL = 32580.4583 VDWAALS =
44898.5089
EELEC = -361745.0234 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 50000 TIME(PS) = 3800.000 TEMP(K) = 0.60 PRESS
= 0.0
Etot = 1.8610 EKtot = 112.4597 EPtot =
112.0440
BOND = 54.8649 ANGLE = 47.2045 DIHED =
13.1249
1-4 NB = 7.4576 1-4 EEL = 76.9887 VDWAALS =
302.3905
EELEC = 400.5069 EHBOND = 0.0000 RESTRAINT =
0.0000
|E(PBS) = 4.5348
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| NonSetup CPU Time in Major Routines:
|
| Routine Sec %
| ------------------------------
| Nonbond 2063.84 94.81
| Bond 0.00 0.00
| Angle 0.00 0.00
| Dihedral 0.00 0.00
| Shake 35.15 1.61
| RunMD 77.85 3.58
| Other 0.02 0.00
| ------------------------------
| Total 2176.87
| 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 0.01 0.00
| ---------------------------------
| Total 0.01 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) = 2264.91 Per Step(ms) = 45.30
| ns/day = 3.81 seconds/ns = 22649.07
| -----------------------------------------------------
| Setup CPU time: 0.83 seconds
| NonSetup CPU time: 2176.87 seconds
| Total CPU time: 2177.70 seconds 0.60 hours
| Setup wall time: 1 seconds
| NonSetup wall time: 2265 seconds
| Total wall time: 2266 seconds 0.63 hours
Dne Sun, 30 Jan 2011 00:08:41 +0100 peker milas <pekermilas.gmail.com>
napsal/-a:
> I am sorry i just noticed something in NTT=1, NTB=2 without ig=-1
> case. In first 500 ps run i got a smaller trajectory file (1/4 of
> other two 500 ps s). additionally the .out file is 80 times bigger
> than other two. one more thing to say, looks like the first 500 ps
> stopped unexpectedly but consecutive run started using last updated
> coordinates. In other words consecutive runs didn't stop totally and
> they continued to produce something...finally below is the actual
> error which was on stdout,
>
> Error: unspecified launch failure launching kernel kClearForces
> cudaFree GpuBuffer::Deallocate failed unspecified launch failure
>
> best
> peker
>
>
>
> 2011/1/29 peker milas <pekermilas.gmail.com>:
>> Hi Ross and Marek,
>>
>> As a quick update, i run three 1.5 ns simulations with my system. One
>> for NTT=3, NTB=1 case with ig=-1, one for NTT=1, NTB=2 with ig=-1 ,
>> and another one for NTT=1, NTB=2 without ig=-1. None of them produced
>> NaN s. I will continue with other 2 cases. I will let you know about
>> the results...
>>
>> best
>> peker
>>
>> 2011/1/28 Marek Maly <marek.maly.ujep.cz>:
>>> Hi Ross,
>>> I will also do these tests (just short MDs cca 50 000 steps might be
>>> enough I think) soon,
>>> and I will let here know the results.
>>>
>>> Best,
>>>
>>> Marek
>>>
>>>
>>>
>>> Dne Fri, 28 Jan 2011 03:26:48 +0100 Ross Walker <ross.rosswalker.co.uk>
>>> napsal/-a:
>>>
>>>> Hi All,
>>>>
>>>> I am hoping to be able to get some clarity for this thread so that we
>>>> can
>>>> start to look at what might actually be going on here. Right now there
>>>> are a
>>>> lot of theories but no real concrete examples to back things up.
>>>> Specifically I would appreciate it if someone who sees this NAN
>>>> problem
>>>> could take their simulation and run the following:
>>>>
>>>> 1) NTT=3, NTB=2 - This one we already know the problem exists.
>>>>
>>>> 2) NTT=3, NTB=1 - This is NVT and will rule out the barostat if the
>>>> problem
>>>> still exists.
>>>>
>>>> 3) NTT=1, NTB=2 - This is NPT but NOT using the random number stream.
>>>> If
>>>> this crashes it means the problem is likely in the barostat rather
>>>> than
>>>> the
>>>> random number stream.
>>>>
>>>> 4) NTT=1, NTB=1 - This is NVT not using the random number stream. If
>>>> this
>>>> crashes then both my theories are wrong.
>>>>
>>>> 5) NTT=0, NTB=1 - This is NVE, if this crashes then we are in a whole
>>>> world
>>>> of pain...
>>>>
>>>> I want to find out specifically which simulation modes show problems
>>>> and
>>>> which do not. I am 'hoping / assuming' that the problem is restricted
>>>> to
>>>> either NPT calculations or Langevin simulations or possibly NPT with
>>>> Langevin. However, I need someone to carefully try these options and
>>>> document the issue. Everyone's help is greatly appreciated.
>>>>
>>>> All the best
>>>> Ross
>>>>
>>>> /\
>>>> \/
>>>> |\oss Walker
>>>>
>>>> ---------------------------------------------------------
>>>> | Assistant Research Professor |
>>>> | San Diego Supercomputer Center |
>>>> | Adjunct Assistant Professor |
>>>> | Dept. of Chemistry and Biochemistry |
>>>> | University of California San Diego |
>>>> | NVIDIA Fellow |
>>>> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>>>> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
>>>> ---------------------------------------------------------
>>>>
>>>> Note: Electronic Mail is not secure, has no guarantee of delivery, may
>>>> not
>>>> be read every day, and should not be used for urgent or sensitive
>>>> issues.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
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>>>>
>>>>
>>>>
>>>
>>>
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Received on Sat Jan 29 2011 - 19:00:02 PST
