This is a PMEMD simulation output and not a PBSA/GBSA output ... I
thought your problems are with MMPBSA and not with simulations .....
On 02/01/2017 12:46 PM, Albert wrote:
> 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 ?
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Vlad Cojocaru, Ph.D., Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Wed Feb 01 2017 - 05:00:02 PST
