Hi Andreas
&cntrl
nstlim=500000, dt=0.002, ntx=5, irest=1, ntpr=5000, ntwr=10000, ntwx=5000,
temp0=300.0, ntt=1, tautp=2.0, cut=8.,
ntb=2, ntp=1,
ntc=2, ntf=2, tol=0.000001,
nmropt = 1, ioutfm = 1,
&end
&ewald
dsum_tol=0.000001,
/
&wt
type='DUMPFREQ', istep1=50,
&end
&wt
type='END',
&end
DISANG=./Dropbox/PhD/Trastuzumab/Her_Modeller_2_FabHer/TRZ_2016_93/disang.63
DUMPAVE=./Dropbox/PhD/Trastuzumab/Her_Modeller_2_FabHer/TRZ_2016_93/distral_63.
The nmr restraints is what is slowing you down. Having istep1=50 is equivalent to ntpr=50, ntwx=50 and causes the code to have to do a lot more calculation and a lot more I/O forcing CPU to GPU syncs every 50 steps. Set nmropt=0 and I bet you see the expected performance. If you don't need every 50 steps increase it to 5000 to match ntwx and performance should be quite a bit better. If you do need it every 50 steps then there isn't much that can be done I'm afraid.
All the best
Ross
> On Nov 8, 2016, at 04:11, Andreas Tosstorff <andreas.tosstorff.cup.uni-muenchen.de> wrote:
>
> Hi all,
>
>
>
> I am running some simulations for a 240.000 atoms system on a Titan X
> Pascal.
>
>
>
> My 240.000 atoms: 16.01 ns/day.
>
> Ambermd 408609 atoms Cellulose: 18 ns/day.
>
>
>
> When running the smaller DHFR simulation, I achieve however comparable
> results. With my system even outperforming the ambermd benchmark:
>
>
>
> My DHFR: 552.81 ns/day
>
> Ambermd DHFR: 542.58 ns/day
>
>
>
> So I was wondering if there are any parameters I'm missing that have an
> impact on the performance for my larger system.
>
>
>
>
>
> Below are my output files for both runs.
>
>
>
> -----------------------DHFR----------------------------------
>
>
>
>
>
> -------------------------------------------------------
>
> Amber 16 PMEMD 2016
>
> -------------------------------------------------------
>
>
>
> | PMEMD implementation of SANDER, Release 16
>
>
>
> | Run on 11/07/2016 at 18:20:59
>
>
>
> | Executable path: pmemd.cuda
>
> | Working directory: /storage/home/WIN/andtos
>
> | Hostname: Unknown
>
> [-O]verwriting output
>
>
>
> File Assignments:
>
> | MDIN: ./Dropbox/PhD/Benchmark/2c2t_md.in
>
>
> | MDOUT: ./Dropbox/PhD/Benchmark/2c2t_md.out
>
>
> | INPCRD: ./Dropbox/PhD/Benchmark/2c2t_min.rst
>
>
> | PARM: ./Dropbox/PhD/Benchmark/2c2t.parm7
>
>
> | RESTRT: ./Dropbox/PhD/Benchmark/2c2t_md.rst
>
>
> | REFC: refc
>
>
> | MDVEL: mdvel
>
>
> | MDEN: mden
>
>
> | MDCRD: mdcrd
>
>
> | MDINFO: mdinfo
>
>
> | MDFRC: mdfrc
>
>
>
>
>
>
> Here is the input file:
>
>
>
> Typical Production MD NVE with
>
>
> GOOD energy conservation, HMR, 4fs.
>
>
> &cntrl
>
>
> ntx=1, irest=0,
>
>
> ntc=2, ntf=2, tol=0.000001,
>
>
> nstlim=75000,
>
>
> ntpr=1000, ntwx=1000,
>
>
> ntwr=10000,
>
>
> dt=0.004, cut=8.,
>
>
> ntt=0, ntb=1, ntp=0,
>
>
> ioutfm=1,
>
>
> /
>
>
> &ewald
>
>
> dsum_tol=0.000001,
>
>
> /
>
>
>
>
>
>
> Note: ig = -1. Setting random seed to 754551 based on wallclock time in
>
> microseconds.
>
> |--------------------- 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 --------------------
>
> |
>
> | CUDA_VISIBLE_DEVICES: not set
>
> | CUDA Capable Devices Detected: 2
>
> | CUDA Device ID in use: 1
>
> | CUDA Device Name: TITAN X (Pascal)
>
> | CUDA Device Global Mem Size: 12189 MB
>
> | CUDA Device Num Multiprocessors: 28
>
> | CUDA Device Core Freq: 1.53 GHz
>
> |
>
> |--------------------------------------------------------
>
>
>
> | Conditional Compilation Defines Used:
>
> | PUBFFT
>
> | BINTRAJ
>
> | CUDA
>
> | EMIL
>
>
>
> | Largest sphere to fit in unit cell has radius = 29.217
>
>
>
> | New format PARM file being parsed.
>
> | Version = 1.000 Date = 11/07/16 Time = 18:20:23
>
>
>
> | 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 = 24304 NTYPES = 16 NBONH = 22802 MBONA = 1537
>
> NTHETH = 3465 MTHETA = 2075 NPHIH = 6892 MPHIA = 6536
>
> NHPARM = 0 NPARM = 0 NNB = 45123 NRES = 7283
>
> NBONA = 1537 NTHETA = 2075 NPHIA = 6536 NUMBND = 71
>
> NUMANG = 161 NPTRA = 201 NATYP = 36 NPHB = 1
>
> IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0
>
> NCOPY = 0
>
>
>
> | Coordinate Index Table dimensions: 14 14 14
>
> | Direct force subcell size = 5.1119 5.1119 5.1119
>
>
>
> BOX TYPE: TRUNCATED OCTAHEDRON
>
>
>
> ----------------------------------------------------------------------------
> ----
>
> 2. CONTROL DATA FOR THE RUN
>
> ----------------------------------------------------------------------------
> ----
>
>
>
> default_name
>
>
>
>
> General flags:
>
> imin = 0, nmropt = 0
>
>
>
> Nature and format of input:
>
> ntx = 1, irest = 0, ntrx = 1
>
>
>
> Nature and format of output:
>
> ntxo = 2, ntpr = 1000, ntrx = 1, ntwr =
> 10000
>
> iwrap = 0, ntwx = 1000, ntwv = 0, ntwe =
> 0
>
> ioutfm = 1, 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 = 8.00000, intdiel = 1.00000
>
>
>
> Frozen or restrained atoms:
>
> ibelly = 0, ntr = 0
>
>
>
> Molecular dynamics:
>
> nstlim = 75000, nscm = 1000, nrespa = 1
>
> t = 0.00000, dt = 0.00400, vlimit = -1.00000
>
>
>
> SHAKE:
>
> ntc = 2, jfastw = 0
>
> tol = 0.00000
>
>
>
> | Intermolecular bonds treatment:
>
> | no_intermolecular_bonds = 1
>
>
>
> | Energy averages sample interval:
>
> | ene_avg_sampling = 1000
>
>
>
> Ewald parameters:
>
> verbose = 0, ew_type = 0, nbflag = 1, use_pme =
> 1
>
> vdwmeth = 1, eedmeth = 1, netfrc = 1
>
> Box X = 71.567 Box Y = 71.567 Box Z = 71.567
>
> Alpha = 109.471 Beta = 109.471 Gamma = 109.471
>
> NFFT1 = 72 NFFT2 = 72 NFFT3 = 72
>
> Cutoff= 8.000 Tol =0.100E-05
>
> Ewald Coefficient = 0.39467
>
> Interpolation order = 4
>
>
>
> ----------------------------------------------------------------------------
> ----
>
> 3. ATOMIC COORDINATES AND VELOCITIES
>
> ----------------------------------------------------------------------------
> ----
>
>
>
> default_name
>
>
> begin time read from input coords = 0.000 ps
>
>
>
> Number of triangulated 3-point waters found: 7097
>
>
>
> Sum of charges from parm topology file = -0.00000007
>
> Forcing neutrality...
>
>
>
> | Dynamic Memory, Types Used:
>
> | Reals 745601
>
> | Integers 812199
>
>
>
> | Nonbonded Pairs Initial Allocation: 4059375
>
>
>
> | GPU memory information (estimate):
>
> | KB of GPU memory in use: 66637
>
> | KB of CPU memory in use: 34224
>
>
>
> ----------------------------------------------------------------------------
> ----
>
> 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 = 0.8987E-11 at 2.875760
>
> ---------------------------------------------------
>
> |---------------------------------------------------
>
> | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
>
> | with 50.0 points per unit in tabled values
>
> | Relative Error Limit not exceeded for r .gt. 2.52
>
> | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
>
> | with 50.0 points per unit in tabled values
>
> | Relative Error Limit not exceeded for r .gt. 2.92
>
> |---------------------------------------------------
>
>
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> 0.0
>
> Etot = -95978.3214 EKtot = 0.0000 EPtot =
> -95978.3214
>
> BOND = 111.6690 ANGLE = 374.5261 DIHED =
> 2117.9406
>
> 1-4 NB = 578.1100 1-4 EEL = 8180.9609 VDWAALS =
> 13099.2755
>
> EELEC = -120440.8034 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000487 0.00(Removed)
>
>
>
> NSTEP = 1000 TIME(PS) = 4.000 TEMP(K) = 72.69 PRESS =
> 0.0
>
> Etot = -83628.9618 EKtot = 3618.7891 EPtot =
> -87247.7508
>
> BOND = 125.7101 ANGLE = 461.9804 DIHED =
> 2177.3242
>
> 1-4 NB = 603.1699 1-4 EEL = 8174.6980 VDWAALS =
> 12930.3395
>
> EELEC = -111720.9728 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000103 0.00(Removed)
>
>
>
> NSTEP = 2000 TIME(PS) = 8.000 TEMP(K) = 77.59 PRESS =
> 0.0
>
> Etot = -83642.1628 EKtot = 3863.0061 EPtot =
> -87505.1689
>
> BOND = 133.4382 ANGLE = 495.6591 DIHED =
> 2171.3048
>
> 1-4 NB = 606.1061 1-4 EEL = 8165.8796 VDWAALS =
> 13249.4005
>
> EELEC = -112326.9571 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000136 0.00(Removed)
>
>
>
> NSTEP = 3000 TIME(PS) = 12.000 TEMP(K) = 81.02 PRESS =
> 0.0
>
> Etot = -83651.0804 EKtot = 4033.5830 EPtot =
> -87684.6634
>
> BOND = 150.2517 ANGLE = 514.5180 DIHED =
> 2189.5612
>
> 1-4 NB = 602.7806 1-4 EEL = 8171.7382 VDWAALS =
> 13168.0116
>
> EELEC = -112481.5248 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000345 0.00(Removed)
>
>
>
> NSTEP = 4000 TIME(PS) = 16.000 TEMP(K) = 82.62 PRESS =
> 0.0
>
> Etot = -83653.3115 EKtot = 4113.2148 EPtot =
> -87766.5263
>
> BOND = 158.1691 ANGLE = 529.9045 DIHED =
> 2192.2796
>
> 1-4 NB = 607.0153 1-4 EEL = 8183.1536 VDWAALS =
> 13385.0126
>
> EELEC = -112822.0610 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000514 0.00(Removed)
>
>
>
> NSTEP = 5000 TIME(PS) = 20.000 TEMP(K) = 82.90 PRESS =
> 0.0
>
> Etot = -83657.1927 EKtot = 4127.2090 EPtot =
> -87784.4017
>
> BOND = 168.8873 ANGLE = 560.4574 DIHED =
> 2201.6659
>
> 1-4 NB = 614.7597 1-4 EEL = 8162.8854 VDWAALS =
> 13379.4005
>
> EELEC = -112872.4580 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000333 0.00(Removed)
>
>
>
> NSTEP = 6000 TIME(PS) = 24.000 TEMP(K) = 83.94 PRESS =
> 0.0
>
> Etot = -83659.4541 EKtot = 4179.2251 EPtot =
> -87838.6792
>
> BOND = 177.1570 ANGLE = 587.6517 DIHED =
> 2182.1998
>
> 1-4 NB = 614.2575 1-4 EEL = 8184.5689 VDWAALS =
> 13341.1927
>
> EELEC = -112925.7068 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000259 0.00(Removed)
>
>
>
>
>
> NSTEP = 49000 TIME(PS) = 196.000 TEMP(K) = 91.15 PRESS =
> 0.0
>
> Etot = -83676.4700 EKtot = 4538.2090 EPtot =
> -88214.6790
>
> BOND = 260.0450 ANGLE = 756.7518 DIHED =
> 2207.6491
>
> 1-4 NB = 622.8510 1-4 EEL = 8174.0375 VDWAALS =
> 13893.8624
>
> EELEC = -114129.8757 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000257 0.00(Removed)
>
>
>
> NSTEP = 50000 TIME(PS) = 200.000 TEMP(K) = 91.67 PRESS =
> 0.0
>
> Etot = -83678.6813 EKtot = 4563.7769 EPtot =
> -88242.4581
>
> BOND = 257.0876 ANGLE = 781.7082 DIHED =
> 2200.4814
>
> 1-4 NB = 609.4546 1-4 EEL = 8172.0605 VDWAALS =
> 13958.7950
>
> EELEC = -114222.0454 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000291 0.00(Removed)
>
>
>
> NSTEP = 51000 TIME(PS) = 204.000 TEMP(K) = 91.43 PRESS =
> 0.0
>
> Etot = -83682.7109 EKtot = 4551.9438 EPtot =
> -88234.6548
>
> BOND = 271.5436 ANGLE = 752.8684 DIHED =
> 2197.5209
>
> 1-4 NB = 608.3235 1-4 EEL = 8181.0471 VDWAALS =
> 14027.6596
>
> EELEC = -114273.6179 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000220 0.00(Removed)
>
>
>
> NSTEP = 52000 TIME(PS) = 208.000 TEMP(K) = 92.20 PRESS =
> 0.0
>
> Etot = -83683.0532 EKtot = 4590.3027 EPtot =
> -88273.3559
>
> BOND = 275.4873 ANGLE = 763.1347 DIHED =
> 2197.0612
>
> 1-4 NB = 615.9724 1-4 EEL = 8162.1206 VDWAALS =
> 14101.1722
>
> EELEC = -114388.3043 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000292 0.00(Removed)
>
>
>
> NSTEP = 53000 TIME(PS) = 212.000 TEMP(K) = 91.95 PRESS =
> 0.0
>
> Etot = -83678.1396 EKtot = 4578.0439 EPtot =
> -88256.1836
>
> BOND = 270.3665 ANGLE = 771.0835 DIHED =
> 2205.8472
>
> 1-4 NB = 618.9741 1-4 EEL = 8181.4440 VDWAALS =
> 13962.6542
>
> EELEC = -114266.5530 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000308 0.00(Removed)
>
>
>
> NSTEP = 54000 TIME(PS) = 216.000 TEMP(K) = 93.04 PRESS =
> 0.0
>
> Etot = -83682.5249 EKtot = 4632.1533 EPtot =
> -88314.6783
>
> BOND = 253.2044 ANGLE = 749.8910 DIHED =
> 2211.2431
>
> 1-4 NB = 620.9964 1-4 EEL = 8170.8711 VDWAALS =
> 13991.6644
>
> EELEC = -114312.5488 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000228 0.00(Removed)
>
>
>
> NSTEP = 55000 TIME(PS) = 220.000 TEMP(K) = 92.51 PRESS =
> 0.0
>
> Etot = -83684.1123 EKtot = 4605.5918 EPtot =
> -88289.7041
>
> BOND = 271.0046 ANGLE = 740.1745 DIHED =
> 2197.9832
>
> 1-4 NB = 611.5845 1-4 EEL = 8155.6705 VDWAALS =
> 13958.9234
>
> EELEC = -114225.0449 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000350 0.00(Removed)
>
>
>
> NSTEP = 56000 TIME(PS) = 224.000 TEMP(K) = 92.42 PRESS =
> 0.0
>
> Etot = -83682.5195 EKtot = 4601.4458 EPtot =
> -88283.9653
>
> BOND = 266.7120 ANGLE = 747.8794 DIHED =
> 2224.5047
>
> 1-4 NB = 607.2874 1-4 EEL = 8184.1817 VDWAALS =
> 13901.9492
>
> EELEC = -114216.4797 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000338 0.00(Removed)
>
>
>
> NSTEP = 57000 TIME(PS) = 228.000 TEMP(K) = 92.14 PRESS =
> 0.0
>
> Etot = -83680.5615 EKtot = 4587.1587 EPtot =
> -88267.7202
>
> BOND = 260.9190 ANGLE = 749.1269 DIHED =
> 2190.8955
>
> 1-4 NB = 618.5479 1-4 EEL = 8169.6077 VDWAALS =
> 13973.1872
>
> EELEC = -114230.0043 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000236 0.00(Removed)
>
>
>
> NSTEP = 58000 TIME(PS) = 232.000 TEMP(K) = 92.26 PRESS =
> 0.0
>
> Etot = -83681.0792 EKtot = 4593.1919 EPtot =
> -88274.2710
>
> BOND = 263.3553 ANGLE = 758.1997 DIHED =
> 2215.2101
>
> 1-4 NB = 608.4316 1-4 EEL = 8168.6263 VDWAALS =
> 14031.7889
>
> EELEC = -114319.8829 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000170 0.00(Removed)
>
>
>
> NSTEP = 59000 TIME(PS) = 236.000 TEMP(K) = 92.44 PRESS =
> 0.0
>
> Etot = -83681.9664 EKtot = 4602.2891 EPtot =
> -88284.2554
>
> BOND = 259.6166 ANGLE = 767.2233 DIHED =
> 2199.2495
>
> 1-4 NB = 615.4153 1-4 EEL = 8165.5614 VDWAALS =
> 13984.7174
>
> EELEC = -114276.0389 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000164 0.00(Removed)
>
>
>
> NSTEP = 60000 TIME(PS) = 240.000 TEMP(K) = 91.98 PRESS =
> 0.0
>
> Etot = -83682.7769 EKtot = 4579.3384 EPtot =
> -88262.1153
>
> BOND = 249.8541 ANGLE = 768.3124 DIHED =
> 2206.7481
>
> 1-4 NB = 615.0716 1-4 EEL = 8182.0497 VDWAALS =
> 13988.6436
>
> EELEC = -114272.7946 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000189 0.00(Removed)
>
>
>
> NSTEP = 61000 TIME(PS) = 244.000 TEMP(K) = 93.15 PRESS =
> 0.0
>
> Etot = -83682.8932 EKtot = 4637.6934 EPtot =
> -88320.5866
>
> BOND = 254.8020 ANGLE = 772.0134 DIHED =
> 2210.5500
>
> 1-4 NB = 620.6896 1-4 EEL = 8160.4999 VDWAALS =
> 14049.1907
>
> EELEC = -114388.3322 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000267 0.00(Removed)
>
>
>
> NSTEP = 62000 TIME(PS) = 248.000 TEMP(K) = 92.73 PRESS =
> 0.0
>
> Etot = -83679.8375 EKtot = 4616.7720 EPtot =
> -88296.6095
>
> BOND = 261.2831 ANGLE = 758.9755 DIHED =
> 2211.3710
>
> 1-4 NB = 614.7107 1-4 EEL = 8175.4674 VDWAALS =
> 13967.2000
>
> EELEC = -114285.6172 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000235 0.00(Removed)
>
>
>
> NSTEP = 63000 TIME(PS) = 252.000 TEMP(K) = 92.93 PRESS =
> 0.0
>
> Etot = -83680.9919 EKtot = 4626.6831 EPtot =
> -88307.6751
>
> BOND = 250.3440 ANGLE = 757.7667 DIHED =
> 2205.4394
>
> 1-4 NB = 609.2522 1-4 EEL = 8149.6342 VDWAALS =
> 14000.9999
>
> EELEC = -114281.1114 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000184 0.00(Removed)
>
>
>
> NSTEP = 64000 TIME(PS) = 256.000 TEMP(K) = 92.83 PRESS =
> 0.0
>
> Etot = -83683.0711 EKtot = 4621.5508 EPtot =
> -88304.6219
>
> BOND = 239.5525 ANGLE = 745.6270 DIHED =
> 2220.8738
>
> 1-4 NB = 617.6087 1-4 EEL = 8172.3025 VDWAALS =
> 13844.9444
>
> EELEC = -114145.5307 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000173 0.00(Removed)
>
>
>
> NSTEP = 65000 TIME(PS) = 260.000 TEMP(K) = 93.01 PRESS =
> 0.0
>
> Etot = -83682.5638 EKtot = 4630.7598 EPtot =
> -88313.3236
>
> BOND = 260.0190 ANGLE = 746.4905 DIHED =
> 2208.5661
>
> 1-4 NB = 624.4461 1-4 EEL = 8176.1744 VDWAALS =
> 13898.9726
>
> EELEC = -114227.9924 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000038 0.00(Removed)
>
>
>
> NSTEP = 66000 TIME(PS) = 264.000 TEMP(K) = 92.64 PRESS =
> 0.0
>
> Etot = -83681.2938 EKtot = 4612.2617 EPtot =
> -88293.5555
>
> BOND = 257.1811 ANGLE = 769.9406 DIHED =
> 2196.7013
>
> 1-4 NB = 626.1907 1-4 EEL = 8157.3730 VDWAALS =
> 14069.7699
>
> EELEC = -114370.7122 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000097 0.00(Removed)
>
>
>
> NSTEP = 67000 TIME(PS) = 268.000 TEMP(K) = 92.61 PRESS =
> 0.0
>
> Etot = -83684.7753 EKtot = 4610.5615 EPtot =
> -88295.3369
>
> BOND = 253.8543 ANGLE = 753.2212 DIHED =
> 2207.1275
>
> 1-4 NB = 621.2360 1-4 EEL = 8179.1783 VDWAALS =
> 13991.5329
>
> EELEC = -114301.4870 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000053 0.00(Removed)
>
>
>
> NSTEP = 68000 TIME(PS) = 272.000 TEMP(K) = 92.25 PRESS =
> 0.0
>
> Etot = -83679.0085 EKtot = 4592.6260 EPtot =
> -88271.6344
>
> BOND = 247.6602 ANGLE = 771.3300 DIHED =
> 2216.5672
>
> 1-4 NB = 616.8963 1-4 EEL = 8194.8695 VDWAALS =
> 14052.3802
>
> EELEC = -114371.3380 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000173 0.00(Removed)
>
>
>
> NSTEP = 69000 TIME(PS) = 276.000 TEMP(K) = 92.74 PRESS =
> 0.0
>
> Etot = -83685.3891 EKtot = 4617.1226 EPtot =
> -88302.5116
>
> BOND = 252.6687 ANGLE = 765.1628 DIHED =
> 2211.9533
>
> 1-4 NB = 608.5757 1-4 EEL = 8163.2522 VDWAALS =
> 13906.7188
>
> EELEC = -114210.8431 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000274 0.00(Removed)
>
>
>
> NSTEP = 70000 TIME(PS) = 280.000 TEMP(K) = 93.10 PRESS =
> 0.0
>
> Etot = -83678.7184 EKtot = 4635.1396 EPtot =
> -88313.8581
>
> BOND = 257.8200 ANGLE = 766.9005 DIHED =
> 2206.5389
>
> 1-4 NB = 621.9698 1-4 EEL = 8183.3024 VDWAALS =
> 13974.4145
>
> EELEC = -114324.8042 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000164 0.00(Removed)
>
>
>
> NSTEP = 71000 TIME(PS) = 284.000 TEMP(K) = 93.49 PRESS =
> 0.0
>
> Etot = -83684.8987 EKtot = 4654.3032 EPtot =
> -88339.2019
>
> BOND = 249.9093 ANGLE = 725.3916 DIHED =
> 2210.9032
>
> 1-4 NB = 620.0760 1-4 EEL = 8210.5792 VDWAALS =
> 13841.0249
>
> EELEC = -114197.0862 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000265 0.00(Removed)
>
>
>
> NSTEP = 72000 TIME(PS) = 288.000 TEMP(K) = 93.76 PRESS =
> 0.0
>
> Etot = -83686.1725 EKtot = 4667.8823 EPtot =
> -88354.0548
>
> BOND = 257.4239 ANGLE = 737.9259 DIHED =
> 2207.0769
>
> 1-4 NB = 610.9468 1-4 EEL = 8190.1325 VDWAALS =
> 13924.2696
>
> EELEC = -114281.8304 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000179 0.00(Removed)
>
>
>
> NSTEP = 73000 TIME(PS) = 292.000 TEMP(K) = 93.11 PRESS =
> 0.0
>
> Etot = -83683.4873 EKtot = 4635.7412 EPtot =
> -88319.2285
>
> BOND = 259.7581 ANGLE = 759.5119 DIHED =
> 2202.1605
>
> 1-4 NB = 603.1771 1-4 EEL = 8186.0657 VDWAALS =
> 14086.0266
>
> EELEC = -114415.9283 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000222 0.00(Removed)
>
>
>
> NSTEP = 74000 TIME(PS) = 296.000 TEMP(K) = 93.53 PRESS =
> 0.0
>
> Etot = -83681.9285 EKtot = 4656.5522 EPtot =
> -88338.4808
>
> BOND = 262.9754 ANGLE = 769.8954 DIHED =
> 2196.6080
>
> 1-4 NB = 611.0025 1-4 EEL = 8164.7565 VDWAALS =
> 14009.2751
>
> EELEC = -114352.9936 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
> check COM velocity, temp: 0.000137 0.00(Removed)
>
>
>
> NSTEP = 75000 TIME(PS) = 300.000 TEMP(K) = 93.57 PRESS =
> 0.0
>
> Etot = -83684.5976 EKtot = 4658.5552 EPtot =
> -88343.1528
>
> BOND = 256.6035 ANGLE = 777.0333 DIHED =
> 2207.7610
>
> 1-4 NB = 623.0649 1-4 EEL = 8176.3008 VDWAALS =
> 13948.7081
>
> EELEC = -114332.6242 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
>
>
> A V E R A G E S O V E R 75 S T E P S
>
>
>
>
>
> NSTEP = 75000 TIME(PS) = 300.000 TEMP(K) = 89.78 PRESS =
> 0.0
>
> Etot = -83676.6057 EKtot = 4469.9454 EPtot =
> -88146.5511
>
> BOND = 239.2836 ANGLE = 718.2113 DIHED =
> 2204.9564
>
> 1-4 NB = 614.5756 1-4 EEL = 8173.7806 VDWAALS =
> 13799.7408
>
> EELEC = -113897.0993 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> ----------------------------------------------------------------------------
> --
>
>
>
>
>
> R M S F L U C T U A T I O N S
>
>
>
>
>
> NSTEP = 75000 TIME(PS) = 300.000 TEMP(K) = 3.75 PRESS =
> 0.0
>
> Etot = 10.2132 EKtot = 186.6720 EPtot =
> 196.5398
>
> BOND = 31.3975 ANGLE = 68.9747 DIHED =
> 9.9859
>
> 1-4 NB = 5.9357 1-4 EEL = 13.2575 VDWAALS =
> 238.0087
>
> EELEC = 530.3662 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> |E(PBS) = 44.6263
>
> ----------------------------------------------------------------------------
> --
>
>
>
> ----------------------------------------------------------------------------
> ----
>
> 5. TIMINGS
>
> ----------------------------------------------------------------------------
> ----
>
>
>
> | NonSetup CPU Time in Major Routines:
>
> |
>
> | Routine Sec %
>
> | ------------------------------
>
> | Nonbond 10.34 22.72
>
> | Bond 0.00 0.00
>
> | Angle 0.00 0.00
>
> | Dihedral 0.00 0.00
>
> | Shake 0.86 1.90
>
> | RunMD 34.16 75.06
>
> | Other 0.15 0.32
>
> | ------------------------------
>
> | Total 45.51
>
>
>
> | 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 0.08 0.17
>
> | ---------------------------------
>
> | Total 0.08 0.17
>
>
>
> | 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 75000 steps:
>
> | Elapsed(s) = 46.89 Per Step(ms) = 0.63
>
> | ns/day = 552.81 seconds/ns = 156.29
>
> |
>
> | Average timings for all steps:
>
> | Elapsed(s) = 46.89 Per Step(ms) = 0.63
>
> | ns/day = 552.81 seconds/ns = 156.29
>
> | -----------------------------------------------------
>
>
>
> | Setup CPU time: 1.00 seconds
>
> | NonSetup CPU time: 45.51 seconds
>
> | Total CPU time: 46.51 seconds 0.01 hours
>
>
>
> | Setup wall time: 1 seconds
>
> | NonSetup wall time: 47 seconds
>
> | Total wall time: 48 seconds 0.01 hours
>
>
>
>
>
> --------------------------------------240000
> System--------------------------
>
>
>
>
>
>
>
> -------------------------------------------------------
>
> Amber 16 PMEMD 2016
>
> -------------------------------------------------------
>
>
>
> | PMEMD implementation of SANDER, Release 16
>
>
>
> | Run on 11/07/2016 at 21:33:39
>
>
>
> | Executable path: pmemd.cuda
>
> | Working directory: /storage/home/WIN/andtos
>
> | Hostname: Unknown
>
> [-O]verwriting output
>
>
>
> File Assignments:
>
> | MDIN:
> ./Dropbox/PhD/Trastuzumab/Her_Modeller_2_FabHer/TRZ_2016_93/mdin_prod.
>
> | MDOUT:
> ./Dropbox/PhD/Trastuzumab/Her_Modeller_2_FabHer/TRZ_2016_93/TRZ_2016_9
>
> | INPCRD:
> ./Dropbox/PhD/Trastuzumab/Her_Modeller_2_FabHer/TRZ_2016_93/TRZ_2016_9
>
> | PARM:
> ./Dropbox/PhD/Trastuzumab/Her_Modeller_2_FabHer/TRZ_2016_93/TRZ_2016_9
>
> | RESTRT:
> ./Dropbox/PhD/Trastuzumab/Her_Modeller_2_FabHer/TRZ_2016_93/TRZ_2016_9
>
> | REFC: refc
>
>
> | MDVEL: mdvel
>
>
> | MDEN: mden
>
>
> | MDCRD:
> ./Dropbox/PhD/Trastuzumab/Her_Modeller_2_FabHer/TRZ_2016_93/TRZ_2016_9
>
> | MDINFO: mdinfo
>
>
> | MDFRC: mdfrc
>
>
>
>
>
>
> Here is the input file:
>
>
>
> 200 ps NPT production for 63 A
>
>
> Constant pressure constant temperature production run
>
>
> &cntrl
>
>
> nstlim=500000, dt=0.002, ntx=5, irest=1, ntpr=5000, ntwr=10000, ntwx=5000,
>
>
> temp0=300.0, ntt=1, tautp=2.0, cut=8.,
>
>
>
>
>
> ntb=2, ntp=1,
>
>
>
>
>
> ntc=2, ntf=2, tol=0.000001,
>
>
>
>
>
> nmropt = 1, ioutfm = 1,
>
>
>
>
>
> &end
>
>
>
>
>
> &ewald
>
>
> dsum_tol=0.000001,
>
>
> /
>
>
>
>
>
> &wt
>
>
> type='DUMPFREQ', istep1=50,
>
>
> &end
>
>
> &wt
>
>
> type='END',
>
>
> &end
>
>
> DISANG=./Dropbox/PhD/Trastuzumab/Her_Modeller_2_FabHer/TRZ_2016_93/disang.63
>
>
> DUMPAVE=./Dropbox/PhD/Trastuzumab/Her_Modeller_2_FabHer/TRZ_2016_93/distral_
> 63.
>
>
>
>
>
> Note: ig = -1. Setting random seed to 402342 based on wallclock time in
>
> microseconds.
>
> |--------------------- 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 --------------------
>
> |
>
> | CUDA_VISIBLE_DEVICES: not set
>
> | CUDA Capable Devices Detected: 2
>
> | CUDA Device ID in use: 1
>
> | CUDA Device Name: TITAN X (Pascal)
>
> | CUDA Device Global Mem Size: 12189 MB
>
> | CUDA Device Num Multiprocessors: 28
>
> | CUDA Device Core Freq: 1.53 GHz
>
> |
>
> |--------------------------------------------------------
>
>
>
> | Conditional Compilation Defines Used:
>
> | PUBFFT
>
> | BINTRAJ
>
> | CUDA
>
> | EMIL
>
>
>
> | Largest sphere to fit in unit cell has radius = 42.715
>
>
>
> | New format PARM file being parsed.
>
> | Version = 1.000 Date = 11/01/16 Time = 14:20:36
>
>
>
> | 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 = 237560 NTYPES = 17 NBONH = 230892 MBONA = 6826
>
> NTHETH = 14656 MTHETA = 9302 NPHIH = 30538 MPHIA = 29664
>
> NHPARM = 0 NPARM = 0 NNB = 371832 NRES = 75696
>
> NBONA = 6826 NTHETA = 9302 NPHIA = 29664 NUMBND = 70
>
> NUMANG = 160 NPTRA = 203 NATYP = 35 NPHB = 1
>
> IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
>
> NCOPY = 0
>
>
>
> | Coordinate Index Table dimensions: 18 36 38
>
> | Direct force subcell size = 4.7462 4.6011 4.5090
>
>
>
> BOX TYPE: RECTILINEAR
>
>
>
> ----------------------------------------------------------------------------
> ----
>
> 2. CONTROL DATA FOR THE RUN
>
> ----------------------------------------------------------------------------
> ----
>
>
>
> default_name
>
>
>
>
> General flags:
>
> imin = 0, nmropt = 1
>
>
>
> Nature and format of input:
>
> ntx = 5, irest = 1, ntrx = 1
>
>
>
> Nature and format of output:
>
> ntxo = 2, ntpr = 5000, ntrx = 1, ntwr =
> 10000
>
> 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 = 8.00000, 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
>
>
>
> Berendsen (weak-coupling) temperature regulation:
>
> temp0 = 300.00000, tempi = 0.00000, tautp = 2.00000
>
>
>
> Pressure regulation:
>
> ntp = 1
>
> pres0 = 1.00000, comp = 44.60000, taup = 1.00000
>
>
>
> SHAKE:
>
> ntc = 2, jfastw = 0
>
> tol = 0.00000
>
>
>
> NMR refinement options:
>
> iscale = 0, noeskp = 1, ipnlty = 1, mxsub =
> 1
>
> scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
>
>
>
> | 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 = 85.431 Box Y = 165.641 Box Z = 171.343
>
> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
>
> NFFT1 = 96 NFFT2 = 168 NFFT3 = 180
>
> Cutoff= 8.000 Tol =0.100E-05
>
> Ewald Coefficient = 0.39467
>
> Interpolation order = 4
>
>
>
> ----------------------------------------------------------------------------
> ----
>
> 3. ATOMIC COORDINATES AND VELOCITIES
>
> ----------------------------------------------------------------------------
> ----
>
>
>
> default_name
>
>
> begin time read from input coords = 500.000 ps
>
>
>
>
>
>
>
> Begin reading energy term weight changes/NMR restraints
>
> WEIGHT CHANGES:
>
> DUMPFREQ 50 0 0.000000 0.000000 0 0
>
> ** No weight changes given **
>
>
>
> RESTRAINTS:
>
> Requested file redirections:
>
> DISANG =
> ./Dropbox/PhD/Trastuzumab/Her_Modeller_2_FabHer/TRZ_2016_93/disang.63
>
> DUMPAVE =
> ./Dropbox/PhD/Trastuzumab/Her_Modeller_2_FabHer/TRZ_2016_93/distral_63.d
>
> Restraints will be read from file:
> ./Dropbox/PhD/Trastuzumab/Her_Modeller_2_FabHer/TRZ_2016_93/disang.63
>
> Here are comments from the DISANG input file:
>
>
>
> Number of restraints read = 1
>
>
>
> Done reading weight changes/NMR restraints
>
>
>
>
>
> Number of triangulated 3-point waters found: 74808
>
>
>
> Sum of charges from parm topology file = -0.00000063
>
> Forcing neutrality...
>
>
>
> | Dynamic Memory, Types Used:
>
> | Reals 9342683
>
> | Integers 6974732
>
>
>
> | Nonbonded Pairs Initial Allocation: 39678459
>
>
>
> | GPU memory information (estimate):
>
> | KB of GPU memory in use: 545960
>
> | KB of CPU memory in use: 255089
>
>
>
> ----------------------------------------------------------------------------
> ----
>
> 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 = 0.8987E-11 at 2.875760
>
> ---------------------------------------------------
>
> |---------------------------------------------------
>
> | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
>
> | with 50.0 points per unit in tabled values
>
> | Relative Error Limit not exceeded for r .gt. 2.52
>
> | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
>
> | with 50.0 points per unit in tabled values
>
> | Relative Error Limit not exceeded for r .gt. 2.92
>
> |---------------------------------------------------
>
> check COM velocity, temp: 0.000709 0.00(Removed)
>
> check COM velocity, temp: 0.000007 0.00(Removed)
>
> check COM velocity, temp: 0.000023 0.00(Removed)
>
> check COM velocity, temp: 0.000012 0.00(Removed)
>
> check COM velocity, temp: 0.000014 0.00(Removed)
>
>
>
> NSTEP = 5000 TIME(PS) = 510.000 TEMP(K) = 301.00 PRESS =
> -8.9
>
> Etot = -583426.5852 EKtot = 144088.3125 EPtot =
> -727514.8977
>
> BOND = 2411.3904 ANGLE = 6575.2942 DIHED =
> 10924.3112
>
> 1-4 NB = 2986.6906 1-4 EEL = 37777.8614 VDWAALS =
> 101938.5885
>
> EELEC = -890129.0621 EHBOND = 0.0000 RESTRAINT =
> 0.0282
>
> EAMBER (non-restraint) = -727514.9258
>
> EKCMT = 67518.3748 VIRIAL = 67984.6864 VOLUME =
> 2425373.0425
>
> Density =
> 0.9878
>
> ----------------------------------------------------------------------------
> --
>
>
>
> NMR restraints: Bond = 0.028 Angle = 0.000 Torsion = 0.000
>
> ============================================================================
> ===
>
> check COM velocity, temp: 0.000003 0.00(Removed)
>
> check COM velocity, temp: 0.000009 0.00(Removed)
>
> check COM velocity, temp: 0.000019 0.00(Removed)
>
> check COM velocity, temp: 0.000007 0.00(Removed)
>
> check COM velocity, temp: 0.000011 0.00(Removed)
>
>
>
> NSTEP = 10000 TIME(PS) = 520.000 TEMP(K) = 299.79 PRESS =
> 56.0
>
> Etot = -583429.1779 EKtot = 143508.9062 EPtot =
> -726938.0841
>
> BOND = 2543.0911 ANGLE = 6528.6244 DIHED =
> 10924.5879
>
> 1-4 NB = 2924.9081 1-4 EEL = 37597.3950 VDWAALS =
> 101766.8935
>
> EELEC = -889224.2185 EHBOND = 0.0000 RESTRAINT =
> 0.6345
>
> EAMBER (non-restraint) = -726938.7187
>
> EKCMT = 67254.8340 VIRIAL = 64320.4999 VOLUME =
> 2424852.8794
>
> Density =
> 0.9880
>
> ----------------------------------------------------------------------------
> --
>
>
>
>
>
> NMR restraints: Bond = 0.790 Angle = 0.000 Torsion = 0.000
>
> ============================================================================
> ===
>
> check COM velocity, temp: 0.000024 0.00(Removed)
>
> check COM velocity, temp: 0.000008 0.00(Removed)
>
> check COM velocity, temp: 0.000022 0.00(Removed)
>
> check COM velocity, temp: 0.000043 0.00(Removed)
>
> check COM velocity, temp: 0.000017 0.00(Removed)
>
>
>
> NSTEP = 40000 TIME(PS) = 580.000 TEMP(K) = 300.87 PRESS =
> -28.7
>
> Etot = -583156.3506 EKtot = 144027.8594 EPtot =
> -727184.2100
>
> BOND = 2428.8020 ANGLE = 6373.5315 DIHED =
> 10866.5979
>
> 1-4 NB = 2961.7757 1-4 EEL = 37626.7203 VDWAALS =
> 101893.9364
>
> EELEC = -889335.5749 EHBOND = 0.0000 RESTRAINT =
> 0.0012
>
> EAMBER (non-restraint) = -727184.2112
>
> EKCMT = 67879.2284 VIRIAL = 69383.9613 VOLUME =
> 2425363.1708
>
> Density =
> 0.9878
>
> ----------------------------------------------------------------------------
> --
>
>
>
>
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ============================================================================
> ===
>
> check COM velocity, temp: 0.000030 0.00(Removed)
>
> check COM velocity, temp: 0.000027 0.00(Removed)
>
> check COM velocity, temp: 0.000016 0.00(Removed)
>
> check COM velocity, temp: 0.000031 0.00(Removed)
>
> check COM velocity, temp: 0.000027 0.00(Removed)
>
>
>
> NSTEP = 445000 TIME(PS) = 1390.000 TEMP(K) = 299.28 PRESS =
> -20.7
>
> Etot = -583367.8274 EKtot = 143267.2344 EPtot =
> -726635.0618
>
> BOND = 2460.4063 ANGLE = 6568.2509 DIHED =
> 10909.4730
>
> 1-4 NB = 2971.8806 1-4 EEL = 37555.3302 VDWAALS =
> 101599.8766
>
> EELEC = -888701.0002 EHBOND = 0.0000 RESTRAINT =
> 0.7209
>
> EAMBER (non-restraint) = -726635.7827
>
> EKCMT = 67239.0759 VIRIAL = 68324.6566 VOLUME =
> 2425529.1213
>
> Density =
> 0.9877
>
> ----------------------------------------------------------------------------
> --
>
>
>
> NMR restraints: Bond = 0.721 Angle = 0.000 Torsion = 0.000
>
> ============================================================================
> ===
>
> check COM velocity, temp: 0.000029 0.00(Removed)
>
> check COM velocity, temp: 0.000026 0.00(Removed)
>
> check COM velocity, temp: 0.000028 0.00(Removed)
>
> check COM velocity, temp: 0.000016 0.00(Removed)
>
> check COM velocity, temp: 0.000024 0.00(Removed)
>
>
>
> NSTEP = 450000 TIME(PS) = 1400.000 TEMP(K) = 299.75 PRESS =
> -32.3
>
> Etot = -583485.5216 EKtot = 143488.4219 EPtot =
> -726973.9434
>
> BOND = 2425.2339 ANGLE = 6439.1236 DIHED =
> 10883.5475
>
> 1-4 NB = 2929.6868 1-4 EEL = 37556.9613 VDWAALS =
> 101519.2403
>
> EELEC = -888727.7467 EHBOND = 0.0000 RESTRAINT =
> 0.0099
>
> EAMBER (non-restraint) = -726973.9533
>
> EKCMT = 67535.1148 VIRIAL = 69225.2684 VOLUME =
> 2424452.5393
>
> Density =
> 0.9881
>
> ----------------------------------------------------------------------------
> --
>
>
>
> NMR restraints: Bond = 0.010 Angle = 0.000 Torsion = 0.000
>
> ============================================================================
> ===
>
> check COM velocity, temp: 0.000006 0.00(Removed)
>
> check COM velocity, temp: 0.000028 0.00(Removed)
>
> check COM velocity, temp: 0.000005 0.00(Removed)
>
> check COM velocity, temp: 0.000024 0.00(Removed)
>
> check COM velocity, temp: 0.000012 0.00(Removed)
>
>
>
> NSTEP = 455000 TIME(PS) = 1410.000 TEMP(K) = 300.09 PRESS =
> 2.9
>
> Etot = -583560.6779 EKtot = 143652.5000 EPtot =
> -727213.1779
>
> BOND = 2446.8756 ANGLE = 6449.9512 DIHED =
> 10857.9126
>
> 1-4 NB = 2945.6408 1-4 EEL = 37626.2206 VDWAALS =
> 101714.3762
>
> EELEC = -889254.2061 EHBOND = 0.0000 RESTRAINT =
> 0.0512
>
> EAMBER (non-restraint) = -727213.2291
>
> EKCMT = 67352.9578 VIRIAL = 67202.6006 VOLUME =
> 2422655.2974
>
> Density =
> 0.9889
>
> ----------------------------------------------------------------------------
> --
>
>
>
> NMR restraints: Bond = 0.051 Angle = 0.000 Torsion = 0.000
>
> ============================================================================
> ===
>
> check COM velocity, temp: 0.000037 0.00(Removed)
>
> check COM velocity, temp: 0.000016 0.00(Removed)
>
> check COM velocity, temp: 0.000018 0.00(Removed)
>
> check COM velocity, temp: 0.000013 0.00(Removed)
>
> check COM velocity, temp: 0.000014 0.00(Removed)
>
>
>
> NSTEP = 460000 TIME(PS) = 1420.000 TEMP(K) = 299.57 PRESS =
> -9.4
>
> Etot = -583579.4939 EKtot = 143402.8438 EPtot =
> -726982.3376
>
> BOND = 2560.1740 ANGLE = 6402.3817 DIHED =
> 10851.2438
>
> 1-4 NB = 2953.5230 1-4 EEL = 37665.3074 VDWAALS =
> 101068.2431
>
> EELEC = -888484.0765 EHBOND = 0.0000 RESTRAINT =
> 0.8660
>
> EAMBER (non-restraint) = -726983.2036
>
> EKCMT = 67038.9020 VIRIAL = 67530.9966 VOLUME =
> 2421554.1060
>
> Density =
> 0.9893
>
> ----------------------------------------------------------------------------
> --
>
>
>
> NMR restraints: Bond = 0.866 Angle = 0.000 Torsion = 0.000
>
> ============================================================================
> ===
>
> check COM velocity, temp: 0.000005 0.00(Removed)
>
> check COM velocity, temp: 0.000030 0.00(Removed)
>
> check COM velocity, temp: 0.000014 0.00(Removed)
>
> check COM velocity, temp: 0.000016 0.00(Removed)
>
> check COM velocity, temp: 0.000033 0.00(Removed)
>
>
>
> NSTEP = 465000 TIME(PS) = 1430.000 TEMP(K) = 300.08 PRESS =
> -15.7
>
> Etot = -583582.6762 EKtot = 143647.4219 EPtot =
> -727230.0981
>
> BOND = 2549.6391 ANGLE = 6499.1456 DIHED =
> 10852.2084
>
> 1-4 NB = 2938.9084 1-4 EEL = 37535.9829 VDWAALS =
> 101133.8505
>
> EELEC = -888740.3070 EHBOND = 0.0000 RESTRAINT =
> 0.4741
>
> EAMBER (non-restraint) = -727230.5723
>
> EKCMT = 67698.5799 VIRIAL = 68518.1682 VOLUME =
> 2425240.1684
>
> Density =
> 0.9878
>
> ----------------------------------------------------------------------------
> --
>
>
>
> NMR restraints: Bond = 0.474 Angle = 0.000 Torsion = 0.000
>
> ============================================================================
> ===
>
> check COM velocity, temp: 0.000030 0.00(Removed)
>
> check COM velocity, temp: 0.000035 0.00(Removed)
>
> check COM velocity, temp: 0.000016 0.00(Removed)
>
> check COM velocity, temp: 0.000026 0.00(Removed)
>
> check COM velocity, temp: 0.000015 0.00(Removed)
>
>
>
> NSTEP = 470000 TIME(PS) = 1440.000 TEMP(K) = 300.02 PRESS =
> 8.4
>
> Etot = -583726.1146 EKtot = 143617.6562 EPtot =
> -727343.7709
>
> BOND = 2435.9157 ANGLE = 6584.2141 DIHED =
> 10891.6130
>
> 1-4 NB = 2975.6154 1-4 EEL = 37579.9380 VDWAALS =
> 101922.0598
>
> EELEC = -889734.8197 EHBOND = 0.0000 RESTRAINT =
> 1.6929
>
> EAMBER (non-restraint) = -727345.4637
>
> EKCMT = 67276.4848 VIRIAL = 66838.2977 VOLUME =
> 2422698.7705
>
> Density =
> 0.9888
>
> ----------------------------------------------------------------------------
> --
>
>
>
> NMR restraints: Bond = 1.693 Angle = 0.000 Torsion = 0.000
>
> ============================================================================
> ===
>
> check COM velocity, temp: 0.000018 0.00(Removed)
>
> check COM velocity, temp: 0.000032 0.00(Removed)
>
> check COM velocity, temp: 0.000022 0.00(Removed)
>
> check COM velocity, temp: 0.000018 0.00(Removed)
>
> check COM velocity, temp: 0.000021 0.00(Removed)
>
>
>
> NSTEP = 475000 TIME(PS) = 1450.000 TEMP(K) = 300.61 PRESS =
> 10.3
>
> Etot = -583577.7926 EKtot = 143904.2031 EPtot =
> -727481.9958
>
> BOND = 2487.1492 ANGLE = 6432.8062 DIHED =
> 10856.2220
>
> 1-4 NB = 2938.9757 1-4 EEL = 37650.2697 VDWAALS =
> 102196.3844
>
> EELEC = -890043.8582 EHBOND = 0.0000 RESTRAINT =
> 0.0552
>
> EAMBER (non-restraint) = -727482.0510
>
> EKCMT = 67378.7643 VIRIAL = 66839.1539 VOLUME =
> 2425083.5180
>
> Density =
> 0.9879
>
> ----------------------------------------------------------------------------
> --
>
>
>
> NMR restraints: Bond = 0.055 Angle = 0.000 Torsion = 0.000
>
> ============================================================================
> ===
>
> check COM velocity, temp: 0.000017 0.00(Removed)
>
> check COM velocity, temp: 0.000021 0.00(Removed)
>
> check COM velocity, temp: 0.000019 0.00(Removed)
>
> check COM velocity, temp: 0.000023 0.00(Removed)
>
> check COM velocity, temp: 0.000028 0.00(Removed)
>
>
>
> NSTEP = 480000 TIME(PS) = 1460.000 TEMP(K) = 299.19 PRESS =
> 121.2
>
> Etot = -583521.5779 EKtot = 143224.1719 EPtot =
> -726745.7498
>
> BOND = 2474.7239 ANGLE = 6427.4124 DIHED =
> 10873.5902
>
> 1-4 NB = 2931.8030 1-4 EEL = 37629.7202 VDWAALS =
> 102321.8948
>
> EELEC = -889404.9305 EHBOND = 0.0000 RESTRAINT =
> 0.0363
>
> EAMBER (non-restraint) = -726745.7861
>
> EKCMT = 67133.5011 VIRIAL = 60792.5776 VOLUME =
> 2423113.2470
>
> Density =
> 0.9887
>
> ----------------------------------------------------------------------------
> --
>
>
>
> NMR restraints: Bond = 0.036 Angle = 0.000 Torsion = 0.000
>
> ============================================================================
> ===
>
> check COM velocity, temp: 0.000029 0.00(Removed)
>
> check COM velocity, temp: 0.000030 0.00(Removed)
>
> check COM velocity, temp: 0.000028 0.00(Removed)
>
> check COM velocity, temp: 0.000007 0.00(Removed)
>
> check COM velocity, temp: 0.000013 0.00(Removed)
>
>
>
> NSTEP = 485000 TIME(PS) = 1470.000 TEMP(K) = 299.74 PRESS =
> -17.9
>
> Etot = -583382.3932 EKtot = 143487.7656 EPtot =
> -726870.1589
>
> BOND = 2455.8525 ANGLE = 6417.7771 DIHED =
> 10867.2605
>
> 1-4 NB = 2904.0877 1-4 EEL = 37722.4489 VDWAALS =
> 101360.4174
>
> EELEC = -888598.2112 EHBOND = 0.0000 RESTRAINT =
> 0.2083
>
> EAMBER (non-restraint) = -726870.3671
>
> EKCMT = 67301.7343 VIRIAL = 68239.2145 VOLUME =
> 2426758.1399
>
> Density =
> 0.9872
>
> ----------------------------------------------------------------------------
> --
>
>
>
> NMR restraints: Bond = 0.208 Angle = 0.000 Torsion = 0.000
>
> ============================================================================
> ===
>
> check COM velocity, temp: 0.000017 0.00(Removed)
>
> check COM velocity, temp: 0.000018 0.00(Removed)
>
> check COM velocity, temp: 0.000021 0.00(Removed)
>
> check COM velocity, temp: 0.000021 0.00(Removed)
>
> check COM velocity, temp: 0.000014 0.00(Removed)
>
>
>
> NSTEP = 490000 TIME(PS) = 1480.000 TEMP(K) = 300.29 PRESS =
> 13.2
>
> Etot = -583514.8671 EKtot = 143750.0312 EPtot =
> -727264.8984
>
> BOND = 2460.2323 ANGLE = 6430.9124 DIHED =
> 10858.7648
>
> 1-4 NB = 2922.3655 1-4 EEL = 37578.8979 VDWAALS =
> 101687.4587
>
> EELEC = -889203.5948 EHBOND = 0.0000 RESTRAINT =
> 0.0648
>
> EAMBER (non-restraint) = -727264.9632
>
> EKCMT = 67555.6103 VIRIAL = 66866.9070 VOLUME =
> 2424430.6879
>
> Density =
> 0.9881
>
> ----------------------------------------------------------------------------
> --
>
>
>
> NMR restraints: Bond = 0.065 Angle = 0.000 Torsion = 0.000
>
> ============================================================================
> ===
>
> check COM velocity, temp: 0.000027 0.00(Removed)
>
> check COM velocity, temp: 0.000037 0.00(Removed)
>
> check COM velocity, temp: 0.000019 0.00(Removed)
>
> check COM velocity, temp: 0.000027 0.00(Removed)
>
> check COM velocity, temp: 0.000027 0.00(Removed)
>
>
>
> NSTEP = 495000 TIME(PS) = 1490.000 TEMP(K) = 301.57 PRESS =
> -99.9
>
> Etot = -583482.3502 EKtot = 144363.6406 EPtot =
> -727845.9908
>
> BOND = 2469.9403 ANGLE = 6483.8895 DIHED =
> 10871.7995
>
> 1-4 NB = 2960.6924 1-4 EEL = 37576.6710 VDWAALS =
> 101119.1546
>
> EELEC = -889328.2254 EHBOND = 0.0000 RESTRAINT =
> 0.0874
>
> EAMBER (non-restraint) = -727846.0783
>
> EKCMT = 67754.6141 VIRIAL = 72981.9763 VOLUME =
> 2424439.7535
>
> Density =
> 0.9881
>
> ----------------------------------------------------------------------------
> --
>
>
>
> NMR restraints: Bond = 0.087 Angle = 0.000 Torsion = 0.000
>
> ============================================================================
> ===
>
> check COM velocity, temp: 0.000025 0.00(Removed)
>
> check COM velocity, temp: 0.000010 0.00(Removed)
>
> check COM velocity, temp: 0.000023 0.00(Removed)
>
> check COM velocity, temp: 0.000014 0.00(Removed)
>
> check COM velocity, temp: 0.000048 0.00(Removed)
>
>
>
> NSTEP = 500000 TIME(PS) = 1500.000 TEMP(K) = 299.39 PRESS =
> 31.7
>
> Etot = -583440.6474 EKtot = 143320.0938 EPtot =
> -726760.7412
>
> BOND = 2496.2454 ANGLE = 6394.2353 DIHED =
> 10850.7954
>
> 1-4 NB = 2966.9909 1-4 EEL = 37625.2657 VDWAALS =
> 101684.4320
>
> EELEC = -888778.8052 EHBOND = 0.0000 RESTRAINT =
> 0.0993
>
> EAMBER (non-restraint) = -726760.8405
>
> EKCMT = 67272.7750 VIRIAL = 65612.3020 VOLUME =
> 2423361.3665
>
> Density =
> 0.9886
>
> ----------------------------------------------------------------------------
> --
>
>
>
> NMR restraints: Bond = 0.099 Angle = 0.000 Torsion = 0.000
>
> ============================================================================
> ===
>
>
>
> A V E R A G E S O V E R 100 S T E P S
>
>
>
>
>
> NSTEP = 500000 TIME(PS) = 1500.000 TEMP(K) = 300.01 PRESS =
> 2.2
>
> Etot = -583424.8011 EKtot = 143612.6097 EPtot =
> -727037.4108
>
> BOND = 2470.7500 ANGLE = 6444.4494 DIHED =
> 10888.6137
>
> 1-4 NB = 2954.5731 1-4 EEL = 37607.9120 VDWAALS =
> 101754.1528
>
> EELEC = -889158.1626 EHBOND = 0.0000 RESTRAINT =
> 0.3007
>
> EAMBER (non-restraint) = -727037.7115
>
> EKCMT = 67332.8792 VIRIAL = 67215.3502 VOLUME =
> 2424878.1713
>
> Density =
> 0.9880
>
> ----------------------------------------------------------------------------
> --
>
>
>
> NMR restraints: Bond = 0.099 Angle = 0.000 Torsion = 0.000
>
> ============================================================================
> ===
>
>
>
> R M S F L U C T U A T I O N S
>
>
>
>
>
> NSTEP = 500000 TIME(PS) = 1500.000 TEMP(K) = 0.52 PRESS =
> 49.7
>
> Etot = 99.0740 EKtot = 250.9695 EPtot =
> 270.3225
>
> BOND = 41.4968 ANGLE = 60.1593 DIHED =
> 36.6356
>
> 1-4 NB = 23.3731 1-4 EEL = 69.0685 VDWAALS =
> 383.9619
>
> EELEC = 493.1101 EHBOND = 0.0000 RESTRAINT =
> 0.3833
>
> EAMBER (non-restraint) = 269.9393
>
> EKCMT = 188.6404 VIRIAL = 2606.6294 VOLUME =
> 1245.9789
>
> Density =
> 0.0005
>
> ----------------------------------------------------------------------------
> --
>
>
>
>
>
> NMR restraints on final step:
>
>
>
> ----------------------------------------------------------------------------
> ----
>
> 5. TIMINGS
>
> ----------------------------------------------------------------------------
> ----
>
>
>
> | NonSetup CPU Time in Major Routines:
>
> |
>
> | Routine Sec %
>
> | ------------------------------
>
> | Nonbond 4686.16 87.23
>
> | Bond 0.00 0.00
>
> | Angle 0.00 0.00
>
> | Dihedral 0.00 0.00
>
> | Shake 8.36 0.16
>
> | RunMD 675.67 12.58
>
> | Other 1.98 0.04
>
> | ------------------------------
>
> | Total 5372.16
>
>
>
> | 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 1.20 0.02
>
> | ---------------------------------
>
> | Total 1.20 0.02
>
>
>
> | 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 5000 steps:
>
> | Elapsed(s) = 55.33 Per Step(ms) = 11.07
>
> | ns/day = 15.61 seconds/ns = 5533.40
>
> |
>
> | Average timings for all steps:
>
> | Elapsed(s) = 5396.43 Per Step(ms) = 10.79
>
> | ns/day = 16.01 seconds/ns = 5396.43
>
> | -----------------------------------------------------
>
>
>
> | Setup CPU time: 2.31 seconds
>
> | NonSetup CPU time: 5372.16 seconds
>
> | Total CPU time: 5374.47 seconds 1.49 hours
>
>
>
> | Setup wall time: 3 seconds
>
> | NonSetup wall time: 5396 seconds
>
> | Total wall time: 5399 seconds 1.50 hours
>
>
>
>
>
>
>
> ------------------------------------------------------------------
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Nov 08 2016 - 06:00:03 PST
