------------------------------------------------------- Amber 14 SANDER 2014 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 12 | Run on 05/25/2013 at 22:22:51 | WARNING: Stack usage limited by a hard resource limit of 67104768 bytes! | If segment violations occur, get your sysadmin to increase the limit. [-O]verwriting output File Assignments: | MDIN: 1AKI_mdin.0 | MDOUT: 1AKI.solv10.md1.mdout.0 | INPCRD: 1AKI.solv10.equil.rst7.0 | PARM: 1AKI.solv10.parm7 | RESTRT: restrt.000 | REFC: refc | MDVEL: mdvel.000 | MDEN: mden.000 | MDCRD: mdcrd.000 | MDINFO: mdinfo.000 |LOGFILE: logfile.000 Here is the input file: Explicit solvent constant pH MD &cntrl imin=0, irest=1, ntx=5, ntpr=10, ntwx=0, nstlim=10, numexchg=5, dt=0.002, ntt=3, tempi=300, temp0=300, gamma_ln=5.0, ig=10273, ntc=2, ntf=2, cut=8, iwrap=1, ioutfm=1, icnstph=2, ntcnstph=5, solvph=1.0, ntrelax=10, saltcon=0.1, / | Conditional Compilation Defines Used: | DIRFRC_COMTRANS | DIRFRC_EFS | DIRFRC_NOVEC | MPI | PUBFFT | FFTLOADBAL_2PROC | BINTRAJ | Largest sphere to fit in unit cell has radius = 26.098 | New format PARM file being parsed. | Version = 1.000 Date = 12/15/12 Time = 15:13:36 | 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. | INFO: Reading atomic numbers from topology file. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting new box info from bottom of inpcrd NATOM = 19961 NTYPES = 18 NBONH = 18939 MBONA = 1025 NTHETH = 2214 MTHETA = 1389 NPHIH = 4455 MPHIA = 3449 NHPARM = 0 NPARM = 0 NNB = 34856 NRES = 6131 NBONA = 1025 NTHETA = 1389 NPHIA = 3449 NUMBND = 47 NUMANG = 108 NPTRA = 43 NATYP = 30 NPHB = 1 IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are H(N)-modified Bondi radii (mbondi2) |reading charge increments from file: 1AKI.solv10.equil.cpin.0 | Coordinate Index Table dimensions: 11 11 11 | Direct force subcell size = 5.8116 5.8116 5.8116 BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- default_name General flags: imin = 0, nmropt = 0 Replica exchange numexchg= 5, rem= 4 Nature and format of input: ntx = 5, irest = 1, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 10, ntrx = 1, ntwr = 500 iwrap = 1, ntwx = 0, 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 saltcon = 0.10000, offset = 0.09000, gbalpha= 0.80000 gbbeta = 0.00000, gbgamma = 2.90912, surften = 0.00500 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 10, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 10273 temp0 = 300.00000, tempi = 300.00000, gamma_ln= 5.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 Constant pH options: icnstph = 2 ntcnstph = 5 solvph = 1.00000 ntrelax = 10 mccycles = 1 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 10 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 63.927 Box Y = 63.927 Box Z = 63.927 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 64 NFFT2 = 64 NFFT3 = 64 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 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 -------------------------------------------------------------------------------- default_name begin time read from input coords = 4400.000 ps Number of triangulated 3-point waters found: 5981 Sum of charges from parm topology file = -0.00000004 Forcing neutrality... | Dynamic Memory, Types Used: | Reals 1664457 | Integers 1060736 | Nonbonded Pairs Initial Allocation: 2275554 | Running AMBER/MPI version on 2 nodes -------------------------------------------------------------------------------- 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 = 0.8332E-11 at 2.782960 --------------------------------------------------- |--------------------------------------------------- | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.47 | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.89 |--------------------------------------------------- NSTEP = 10 TIME(PS) = 4400.020 TEMP(K) = 303.77 PRESS = 0.0 Etot = -51240.6136 EKtot = 12357.9169 EPtot = -63598.5305 BOND = 396.8190 ANGLE = 995.4379 DIHED = 1348.4826 1-4 NB = 459.9956 1-4 EEL = 3992.8100 VDWAALS = 7520.9430 EELEC = -78313.0185 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2694E-01 SOLVPH = 4.0000 REPNUM = 1 EXCHANGE# = 1 ------------------------------------------------------------------------------ NSTEP = 20 TIME(PS) = 4400.040 TEMP(K) = 302.58 PRESS = 0.0 Etot = -51302.5871 EKtot = 12309.4522 EPtot = -63612.0393 BOND = 378.4900 ANGLE = 992.1172 DIHED = 1379.8535 1-4 NB = 446.6806 1-4 EEL = 4016.4321 VDWAALS = 7410.2676 EELEC = -78235.8803 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2738E-01 SOLVPH = 4.0000 REPNUM = 1 EXCHANGE# = 2 ------------------------------------------------------------------------------ NSTEP = 30 TIME(PS) = 4400.060 TEMP(K) = 271.67 PRESS = 0.0 Etot = -52395.6420 EKtot = 11051.9552 EPtot = -63447.5972 BOND = 387.0255 ANGLE = 1021.1813 DIHED = 1359.6417 1-4 NB = 437.4806 1-4 EEL = 3967.0578 VDWAALS = 7177.3592 EELEC = -77797.3432 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2763E-01 SOLVPH = 4.0000 REPNUM = 1 EXCHANGE# = 3 ------------------------------------------------------------------------------ NSTEP = 40 TIME(PS) = 4400.080 TEMP(K) = 300.52 PRESS = 0.0 Etot = -51273.9401 EKtot = 12225.8425 EPtot = -63499.7826 BOND = 388.9453 ANGLE = 986.1078 DIHED = 1352.5470 1-4 NB = 449.6681 1-4 EEL = 4040.9074 VDWAALS = 7054.2797 EELEC = -77772.2380 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2695E-01 SOLVPH = 4.0000 REPNUM = 1 EXCHANGE# = 4 ------------------------------------------------------------------------------ wrapping first mol.: 21.30915 30.13569 52.19654 NSTEP = 50 TIME(PS) = 4400.100 TEMP(K) = 301.16 PRESS = 0.0 Etot = -51332.7348 EKtot = 12251.7922 EPtot = -63584.5269 BOND = 393.7189 ANGLE = 979.5765 DIHED = 1355.3330 1-4 NB = 440.0561 1-4 EEL = 4037.7458 VDWAALS = 6963.0341 EELEC = -77753.9914 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2730E-01 SOLVPH = 4.0000 REPNUM = 1 EXCHANGE# = 5 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines, Average for All Tasks: | | Routine Sec % | ------------------------------ | DataDistrib 2.16 2.83 | Nonbond 5.64 7.39 | Bond 0.00 0.00 | Angle 0.02 0.03 | Dihedral 0.09 0.12 | Shake 0.05 0.06 | RunMD 54.74 71.72 | Other 13.62 17.84 | ------------------------------ | Total 76.32 | PME Nonbond Pairlist CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | Set Up Cit 15.65 20.50 | Build List 26.65 34.91 | --------------------------------- | Total 42.29 55.41 | PME Direct Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | NonBonded Calc 3.29 4.31 | Exclude Masked 0.08 0.11 | Other 0.16 0.20 | --------------------------------- | Total 3.53 4.63 | PME Reciprocal Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | 1D bspline 34.85 45.65 | Grid Charges 0.28 0.37 | Scalar Sum 0.14 0.18 | Gradient Sum 0.25 0.33 | FFT 0.59 0.77 | --------------------------------- | Total 36.10 47.30 | 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) = 0.01 Per Step(ms) = Infinity | ns/day = 0.00 seconds/ns = Infinity | | Average timings for all steps: | Elapsed(s) = 327.89 Per Step(ms) = 6557.85 | ns/day = 0.03 seconds/ns = 3278923.63 | ----------------------------------------------------- | Master Setup CPU time: 0.29 seconds | Master NonSetup CPU time: 76.80 seconds | Master Total CPU time: 77.09 seconds 0.02 hours | Master Setup wall time: 2 seconds | Master NonSetup wall time: 327 seconds | Master Total wall time: 329 seconds 0.09 hours