------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 10 | Run on 12/12/2008 at 14:55:27 [-O]verwriting output File Assignments: | MDIN: wrap.in | MDOUT: 116_1XCK_apo_temp320_prod54.out | INPCRD: 116_1XCK_apo_temp320_prod53.rst | PARM: 1XCK_sol.prmtop | RESTRT: 116_1XCK_apo_temp320_prod54.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: 116_1XCK_apo_temp320_prod54.mdcrd | MDINFO: mdinfo |LOGFILE: logfile Here is the input file: MD simulation NVE &cntrl imin= 0, irest= 1, ntx = 5, ntb = 1, cut = 10, ntc = 2, ntf = 2, tol = 0.000001, ntt = 0, nstlim = 1, dt = 0.001, ntpr = 1, ntwx = 1, ntwr = 5, ioutfm = 1, iwrap = 1, &ewald dsum_tol = 0.000001, / | Conditional Compilation Defines Used: | DIRFRC_COMTRANS | DIRFRC_EFS | MPI | PUBFFT | BINTRAJ | Largest sphere to fit in unit cell has radius = 86.961 | New format PARM file being parsed. | Version = 1.000 Date = 04/02/08 Time = 00:12:36 | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting new box info from bottom of inpcrd NATOM = 742804 NTYPES = 16 NBONH = 688820 MBONA = 54376 NTHETH = 127246 MTHETA = 73430 NPHIH = 237510 MPHIA = 172886 NHPARM = 0 NPARM = 0 NNB = 1449036 NRES = 218374 NBONA = 54376 NTHETA = 73430 NPHIA = 172886 NUMBND = 37 NUMANG = 73 NPTRA = 43 NATYP = 28 NPHB = 1 IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 31 31 31 | Direct force subcell size = 6.8713 6.8713 6.8713 BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 5, irest = 1, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 5 iwrap = 1, ntwx = 1, 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 = 10.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 1, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00100, vlimit = 20.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00000 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 1 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 213.010 Box Y = 213.010 Box Z = 213.010 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 216 NFFT2 = 216 NFFT3 = 216 Cutoff= 10.000 Tol =0.100E-05 Ewald Coefficient = 0.31234 Interpolation order = 4 | PMEMD ewald parallel performance parameters: | block_fft = 1 | fft_blk_y_divisor = 4 | excl_recip = 1 | excl_master = 1 | atm_redist_freq = 32 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 78400.000 ps Number of triangulated 3-point waters found: 211038 Sum of charges from parm topology file = ************ Assuming uniform neutralizing plasma | Dynamic Memory, Types Used: | Reals 23182840 | Integers 27073501 | Nonbonded Pairs Initial Allocation: 2273676 | Running AMBER/MPI version on 256 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 = 0.8987E-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. 2.33 | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.77 |--------------------------------------------------- wrapping first mol.: -71.003293570940357 -100.41381770288987 173.92186210990866 wrapping first mol.: -71.003293570940357 -100.41381770288987 173.92186210990866 NSTEP = 1 TIME(PS) = 78400.001 TEMP(K) = 319.16 PRESS = 0.0 Etot = -1644461.1000 EKtot = 488222.8505 EPtot = -2132683.9505 BOND = 20478.1308 ANGLE = 54462.0420 DIHED = 76214.5216 1-4 NB = 25195.8983 1-4 EEL = 341301.8217 VDWAALS = 230062.6609 EELEC = -2880399.0259 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.4791E-04 ------------------------------------------------------------------------------ A V E R A G E S O V E R 1 S T E P S NSTEP = 1 TIME(PS) = 78400.001 TEMP(K) = 319.16 PRESS = 0.0 Etot = -1644461.1000 EKtot = 488222.8505 EPtot = -2132683.9505 BOND = 20478.1308 ANGLE = 54462.0420 DIHED = 76214.5216 1-4 NB = 25195.8983 1-4 EEL = 341301.8217 VDWAALS = 230062.6609 EELEC = -2880399.0259 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.4791E-04 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 1 TIME(PS) = 78400.001 TEMP(K) = 0.00 PRESS = 0.0 Etot = 0.0000 EKtot = 0.0000 EPtot = 0.0000 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000 EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000 |E(PBS) = 0.0000 Ewald error estimate: 0.0000E+00 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines, Average for All Tasks: | | Routine Sec % | ------------------------------ | DataDistrib 0.05 16.85 | Nonbond 0.22 67.47 | Bond 0.00 0.00 | Angle 0.00 0.06 | Dihedral 0.00 0.25 | Shake 0.00 0.60 | RunMD 0.05 14.75 | Other 0.00 0.02 | ------------------------------ | Total 0.33 | PME Nonbond Pairlist CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | Set Up Cit 0.12 36.89 | Build List 0.04 12.29 | --------------------------------- | Total 0.16 49.19 | PME Direct Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | NonBonded Calc 0.04 12.73 | Exclude Masked 0.00 0.28 | Other 0.00 1.14 | --------------------------------- | Total 0.05 14.15 | PME Reciprocal Force CPU Time, Average for All Tasks: | | Routine Sec % | --------------------------------- | 1D bspline 0.00 0.23 | Grid Charges 0.00 0.35 | Scalar Sum 0.00 1.33 | Gradient Sum 0.00 0.45 | FFT 0.01 1.77 | --------------------------------- | Total 0.01 4.13 | 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 | Master Setup CPU time: 5.92 seconds | Master NonSetup CPU time: 4.37 seconds | Master Total CPU time: 10.29 seconds 0.00 hours | Master Setup wall time: 7 seconds | Master NonSetup wall time: 4 seconds | Master Total wall time: 11 seconds 0.00 hours