sure. Here it is.
-------------------------------------------------------
Amber 16 PMEMD 2016
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 16
| Run on 02/01/2017 at 11:26:17
| Executable path: pmemd.cuda.MPI
| Working directory: ligand/1
| Hostname: cudaC
[-O]verwriting output
File Assignments:
| MDIN: infile/05-prod.in
| MDOUT: prod4.out
| INPCRD: prod3.rst
| PARM: sol.prmtop
| RESTRT: prod4.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: prod4.nc
| MDINFO: md4.info1
|LOGFILE: logfile
| MDFRC: mdfrc
Here is the input file:
production
&cntrl
imin=0,irest=1,ntx=5,
nstlim=500000,dt=0.002,
ntc=2,ntf=2,
cut=9.0, ntb=2, ntp=1, taup=2.0,
ntpr=5000, ntwx=5000,
ntt=3, gamma_ln=2.0,
temp0=300.0,
/
Note: ig = -1. Setting random seed to 824705 based on wallclock time in
microseconds and disabling the synchronization of random numbers
between tasks to improve performance.
|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 16.0.0
|
| 02/25/2016
|
| Implementation by:
| Ross C. Walker (SDSC)
| Scott Le Grand (nVIDIA)
|
| Precision model in use:
| [SPFP] - Single Precision Forces, 64-bit Fixed Point
| Accumulation. (Default)
|
|--------------------------------------------------------
|----------------- CITATION INFORMATION -----------------
|
| When publishing work that utilized the CUDA version
| of AMBER, please cite the following in addition to
| the regular AMBER citations:
|
| - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan
| Poole; Scott Le Grand; Ross C. Walker "Routine
| microsecond molecular dynamics simulations with
| AMBER - Part II: Particle Mesh Ewald", J. Chem.
| Theory Comput., 2013, 9 (9), pp3878-3888,
| DOI: 10.1021/ct400314y.
|
| - Andreas W. Goetz; Mark J. Williamson; Dong Xu;
| Duncan Poole; Scott Le Grand; Ross C. Walker
| "Routine microsecond molecular dynamics simulations
| with AMBER - Part I: Generalized Born", J. Chem.
| Theory Comput., 2012, 8 (5), pp1542-1555.
|
| - Scott Le Grand; Andreas W. Goetz; Ross C. Walker
| "SPFP: Speed without compromise - a mixed precision
| model for GPU accelerated molecular dynamics
| simulations.", Comp. Phys. Comm., 2013, 184
| pp374-380, DOI: 10.1016/j.cpc.2012.09.022
|
|--------------------------------------------------------
|------------------- GPU DEVICE INFO --------------------
|
| Task ID: 0
| CUDA_VISIBLE_DEVICES: not set
| CUDA Capable Devices Detected: 4
| CUDA Device ID in use: 0
| CUDA Device Name: GeForce GTX TITAN X
| CUDA Device Global Mem Size: 12199 MB
| CUDA Device Num Multiprocessors: 24
| CUDA Device Core Freq: 1.08 GHz
|
|
| Task ID: 1
| CUDA_VISIBLE_DEVICES: not set
| CUDA Capable Devices Detected: 4
| CUDA Device ID in use: 1
| CUDA Device Name: GeForce GTX TITAN X
| CUDA Device Global Mem Size: 12206 MB
| CUDA Device Num Multiprocessors: 24
| CUDA Device Core Freq: 1.08 GHz
|
|--------------------------------------------------------
|---------------- GPU PEER TO PEER INFO -----------------
|
| Peer to Peer support: ENABLED
|
|--------------------------------------------------------
| Conditional Compilation Defines Used:
| MPI
| FFTW_FFT
| BINTRAJ
| MKL
| CUDA
| EMIL
| Largest sphere to fit in unit cell has radius = 47.840
| New format PARM file being parsed.
| Version = 1.000 Date = 02/01/17 Time = 08:51:11
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting box info from netcdf restart file
NATOM = 106304 NTYPES = 20 NBONH = 103196 MBONA = 3122
NTHETH = 40248 MTHETA = 4233 NPHIH = 13937 MPHIA = 13279
NHPARM = 0 NPARM = 0 NNB = 167146 NRES = 33832
NBONA = 3122 NTHETA = 4233 NPHIA = 13279 NUMBND = 86
NUMANG = 198 NPTRA = 208 NATYP = 52 NPHB = 1
IFBOX = 1 NMXRS = 65 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 20 17 17
| Direct force subcell size = 5.6911 5.6282 5.7736
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
UNK
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 2, ntpr = 5000, ntrx = 1, ntwr
= 500000
iwrap = 0, ntwx = 5000, ntwv = 0, ntwe
= 0
ioutfm = 1, 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 = 9.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 500000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -1.00000
Langevin dynamics temperature regulation:
ig = 824705
temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000
Pressure regulation:
ntp = 1
pres0 = 1.00000, comp = 44.60000, taup = 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 = 113.822 Box Y = 95.679 Box Z = 98.151
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 120 NFFT2 = 96 NFFT3 = 100
Cutoff= 9.000 Tol =0.100E-04
Ewald Coefficient = 0.30768
Interpolation order = 4
| PMEMD ewald parallel performance parameters:
| block_fft = 0
| fft_blk_y_divisor = 2
| excl_recip = 0
| excl_master = 0
| atm_redist_freq = 320
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
UNK
begin time read from input coords = 3860.000 ps
Number of triangulated 3-point waters found: 33392
Sum of charges from parm topology file = 0.00099880
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 5530446
| Integers 4658511
| Nonbonded Pairs Initial Allocation: 16077151
| GPU memory information (estimate):
| KB of GPU memory in use: 524904
| KB of CPU memory in use: 137952
| Running AMBER/MPI version on 2 MPI task
--------------------------------------------------------------------------------
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 = 0.3316E-14 at 2.351880
| CHECK d/dx switch(x): max rel err = 0.8205E-11 at 2.761360
---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.39
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.84
|---------------------------------------------------
NSTEP = 5000 TIME(PS) = 3870.000 TEMP(K) = 299.37 PRESS
= -55.5
Etot = -271703.9234 EKtot = 64165.6641 EPtot =
-335869.5875
BOND = 1141.5801 ANGLE = 3163.1115 DIHED = 4887.8726
1-4 NB = 1407.6422 1-4 EEL = 12974.6352 VDWAALS =
44251.1358
EELEC = -403695.5648 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 29927.7249 VIRIAL = 31209.0557 VOLUME =
1069660.5381
Density =
1.0039
------------------------------------------------------------------------------
------------------------------------------------------------------------------
NSTEP = 480000 TIME(PS) = 4820.000 TEMP(K) = 300.79 PRESS
= -47.7
Etot = -270984.1070 EKtot = 64469.1914 EPtot =
-335453.2984
BOND = 1193.7020 ANGLE = 3115.3879 DIHED = 4889.7468
1-4 NB = 1409.5198 1-4 EEL = 12939.5659 VDWAALS =
43945.5001
EELEC = -402946.7210 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 30077.7314 VIRIAL = 31180.1743 VOLUME =
1069947.3851
Density =
1.0036
------------------------------------------------------------------------------
NSTEP = 485000 TIME(PS) = 4830.000 TEMP(K) = 300.27 PRESS
= -10.9
Etot = -271399.0316 EKtot = 64358.9180 EPtot =
-335757.9496
BOND = 1221.4375 ANGLE = 3176.9570 DIHED = 4907.2375
1-4 NB = 1394.1383 1-4 EEL = 12973.3828 VDWAALS =
44721.9992
EELEC = -404153.1021 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 29995.8017 VIRIAL = 30248.2271 VOLUME =
1069085.4142
Density =
1.0044
------------------------------------------------------------------------------
NSTEP = 490000 TIME(PS) = 4840.000 TEMP(K) = 300.18 PRESS
= -2.3
Etot = -271015.9234 EKtot = 64339.9766 EPtot =
-335355.9000
BOND = 1163.8253 ANGLE = 3136.9447 DIHED = 4917.7935
1-4 NB = 1416.5948 1-4 EEL = 13064.3760 VDWAALS =
44138.0466
EELEC = -403193.4809 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 29950.8155 VIRIAL = 30003.3528 VOLUME =
1069281.1986
Density =
1.0042
------------------------------------------------------------------------------
NSTEP = 495000 TIME(PS) = 4850.000 TEMP(K) = 297.97 PRESS
= -71.2
Etot = -271911.3304 EKtot = 63866.0234 EPtot =
-335777.3539
BOND = 1148.4332 ANGLE = 3161.7327 DIHED = 4946.9111
1-4 NB = 1429.9955 1-4 EEL = 13010.2898 VDWAALS =
44198.9242
EELEC = -403673.6404 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 29624.7934 VIRIAL = 31268.5597 VOLUME =
1068741.1051
Density =
1.0047
------------------------------------------------------------------------------
NSTEP = 500000 TIME(PS) = 4860.000 TEMP(K) = 301.85 PRESS
= 15.8
Etot = -270887.2667 EKtot = 64697.3516 EPtot =
-335584.6182
BOND = 1179.9015 ANGLE = 3103.3159 DIHED = 4937.0781
1-4 NB = 1414.7621 1-4 EEL = 13067.3425 VDWAALS =
44229.1523
EELEC = -403516.1705 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 30172.6437 VIRIAL = 29807.3055 VOLUME =
1069387.2208
Density =
1.0041
------------------------------------------------------------------------------
A V E R A G E S O V E R 100 S T E P S
NSTEP = 500000 TIME(PS) = 4860.000 TEMP(K) = 300.08 PRESS
= -1.4
Etot = -271228.7819 EKtot = 64316.5243 EPtot =
-335545.3062
BOND = 1184.2507 ANGLE = 3148.8356 DIHED = 4899.5050
1-4 NB = 1417.0863 1-4 EEL = 13024.9057 VDWAALS =
44246.3505
EELEC = -403466.2400 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 30016.2891 VIRIAL = 30047.8575 VOLUME =
1069177.8363
Density =
1.0043
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 500000 TIME(PS) = 4860.000 TEMP(K) = 0.75 PRESS
= 76.2
Etot = 340.2678 EKtot = 161.2534 EPtot = 276.6869
BOND = 24.7042 ANGLE = 43.9111 DIHED = 24.4974
1-4 NB = 14.4783 1-4 EEL = 55.1055 VDWAALS =
225.0721
EELEC = 397.4438 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 125.7841 VIRIAL = 1745.4171 VOLUME = 701.1236
Density =
0.0007
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| NonSetup CPU Time in Major Routines, Average for All Tasks:
|
| Routine Sec %
| ------------------------------
| DataDistrib 2.22 0.10
| Nonbond 1767.08 82.95
| Bond 0.00 0.00
| Angle 0.00 0.00
| Dihedral 0.00 0.00
| Shake 4.76 0.22
| RunMD 355.26 16.68
| Other 1.11 0.05
| ------------------------------
| Total 2130.42
| PME Nonbond Pairlist CPU Time, Average for All Tasks:
|
| 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, Average for All Tasks:
|
| Routine Sec %
| ---------------------------------
| NonBonded Calc 0.00 0.00
| Exclude Masked 0.00 0.00
| Other 0.73 0.03
| ---------------------------------
| Total 0.73 0.03
| PME Reciprocal Force CPU Time, Average for All Tasks:
|
| 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
| PME Load Balancing CPU Time, Average for All Tasks:
|
| Routine Sec %
| ------------------------------------
| Atom Reassign 0.00 0.00
| Image Reassign 0.00 0.00
| FFT Reassign 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) = 2129.72 Per Step(ms) = 4.26
| ns/day = 40.57 seconds/ns = 2129.72
| -----------------------------------------------------
| Master Setup CPU time: 1.34 seconds
| Master NonSetup CPU time: 2130.47 seconds
| Master Total CPU time: 2131.81 seconds 0.59 hours
| Master Setup wall time: 2 seconds
| Master NonSetup wall time: 2129 seconds
| Master Total wall time: 2131 seconds 0.59 hours
On 02/01/2017 12:21 PM, Vlad Cojocaru wrote:
> Could you post us an mdout file ?
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Received on Wed Feb 01 2017 - 04:00:04 PST
