256 250 MHZ IP27 Processors ------------------------------------------------------- Amber 6 SANDER Scripps/UCSF 1999 ------------------------------------------------------- | Sat Dec 9 19:28:41 2000 [-O]verwriting output File Assignments: |MDIN : /u/ac/jphillip/amber/pme.amber |MDOUT: /u/ac/jphillip/amber/bench_amber_126.log.tmp |INPCR: inpcrd |PARM : prmtop |RESTR: restrt |REFC : refc |MDVEL: mdvel |MDEN : mden |MDCRD: mdcrd |MDINF: mdinfo Here is the input file: short md, nve ensemble &cntrl ntx=1, irest=0, ntc=2, ntf=2, tol=0.0000001, nstlim=500, ntt=0, ntpr=100, ntwr=10000, dt=0.001, vlimit=10.0, tempi=300., temp0 = 300., cut=9., &end &ewald a=62.23, b=62.23, c=62.23, nfft1=64,nfft2=64,nfft3=64, skinnb=2., &end ------------------------------------------------------------------------------- short md, nve ensemble 1. RESOURCE USE: getting box info from bottom of parm getting new box info from bottom of inpcrd | peek_ewald_inpcrd: Box info found EWALD SPECIFIC INPUT: | Using the SGI specific (ZFFT3D) Fast Fourier Transform | Using the T3D specific (FFT3D0) Fast Fourier Transform Largest sphere to fit in unit cell has radius = 31.115 Calculating ew_coeff from dsum_tol,cutoff Box X = 62.230 Box Y = 62.230 Box Z = 62.230 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 64 NFFT2 = 64 NFFT3 = 64 Cutoff= 9.000 Tol =0.100E-04 Ewald Coefficient = 0.30768 Interpolation order = 4 NATOM = 23558 NTYPES = 16 NBONH = 22290 MBONA = 1302 NTHETH = 2789 MTHETA = 1772 NPHIH = 5026 MPHIA = 3140 NHPARM = 0 NPARM = 0 NNB = 41859 NRES = 7182 NBONA = 1302 NTHETA = 1772 NPHIA = 3140 NUMBND = 45 NUMANG = 91 NPTRA = 33 NATYP = 31 NPHB = 1 IFBOX = 1 NMXRS = 25 IFCAP = 0 EWALD MEMORY USE: | Total heap storage needed = 1005 | Adjacent nonbond minimum mask = 41859 | Max number of pointers = 25 | List build maxmask = 83718 | Maximage = 34473 EWALD LOCMEM POINTER OFFSETS | Real memory needed by PME = 1005 | Size of EEDTABLE = 20768 | Real memory needed by EEDTABLE = 83072 | Integer memory needed by ADJ = 83718 | Integer memory used by local nonb= 522891 | Real memory used by local nonb = 386115 | MAX NONBOND PAIRS = 8000000 | Memory Use Allocated Used | Real 4000000 1460123 | Hollerith 1200000 148532 | Integer 4000000 1188556 | Max Nonbonded Pairs: 8000000 BOX TYPE: RECTILINEAR 2. CONTROL DATA FOR THE RUN TIMLIM= 999999. IREST = 0 IBELLY= 0 IMIN = 0 IPOL = 0 NTX = 1 NTXO = 1 IG = 71277 TEMPI = 300.00 HEAT = 0.000 NTB = 1 BOXX = 62.230 BOXY = 62.230 BOXZ = 62.230 NTT = 0 TEMP0 = 300.000 DTEMP = 0.000 TAUTP = 1.000 VLIMIT= 10.000 NTP = 0 PRES0 = 1.000 COMP = 44.600 TAUP = 0.200 NPSCAL= 0 NTCM = 0 NSCM = 9999999 NSTLIM= 500 NTU = 1 T = 0.000 DT = 0.00100 NTC = 2 TOL = 0.00000 JFASTW = 0 NTF = 2 NSNB = 25 CUT = 9.000 SCNB = 2.000 SCEE = 1.200 DIELC = 1.000 NTPR = 100 NTWR = 10000 NTWX = 0 NTWV = 0 NTWE = 0 IOUTFM= 0 NTWPRT= 0 NTWPR0= 0 NTAVE= 0 NTR = 0 NTRX = 1 TAUR = 0.00000 NMROPT= 0 PENCUT= 0.10000 IVCAP = 0 MATCAP= 0 FCAP = 1.500 OTHER DATA: IFCAP = 0 NATCAP= 0 CUTCAP= 0.000 XCAP = 0.000 YCAP = 0.000 ZCAP = 0.000 VRAND= 0 NATOM = 23558 NRES = 7182 Water definition for fast triangulated model: Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ; Hyd2_name = H2 | PLEVEL = 1: runmd parallelization, no EKCMR 3. ATOMIC COORDINATES AND VELOCITIES begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 7023 | Atom division among processors: | 0 188 374 576 762 938 1131 1306 | 1493 1688 1872 2057 2240 2425 2606 2792 | 2978 3164 3350 3536 3722 3908 4094 4280 | 4466 4652 4838 5024 5210 5396 5582 5768 | 5954 6140 6326 6512 6698 6884 7070 7256 | 7442 7628 7814 8000 8186 8372 8558 8744 | 8930 9116 9302 9488 9674 9860 10046 10232 | 10418 10604 10790 10976 11162 11348 11534 11720 | 11906 12092 12278 12464 12650 12836 13022 13208 | 13394 13580 13766 13952 14138 14324 14510 14696 | 14882 15068 15254 15440 15626 15812 15998 16184 | 16370 16556 16742 16928 17114 17300 17486 17672 | 17858 18044 18230 18416 18602 18788 18974 19160 | 19346 19532 19718 19904 20090 20276 20462 20648 | 20834 21020 21206 21392 21578 21764 21950 22136 | 22322 22508 22694 22880 23066 23252 23558 | Atom division among processors for gb: | 0 186 372 558 744 930 1116 1302 | 1488 1674 1860 2046 2232 2418 2604 2790 | 2976 3162 3348 3534 3720 3906 4092 4278 | 4464 4650 4836 5022 5208 5394 5580 5766 | 5952 6138 6324 6510 6696 6882 7068 7254 | 7440 7626 7812 7998 8184 8370 8556 8742 | 8928 9114 9300 9486 9672 9858 10044 10230 | 10416 10602 10788 10974 11160 11346 11532 11718 | 11904 12090 12276 12462 12648 12834 13020 13206 | 13392 13578 13764 13950 14136 14322 14508 14694 | 14880 15066 15252 15438 15624 15810 15996 16182 | 16368 16554 16740 16926 17112 17298 17484 17670 | 17856 18042 18228 18414 18600 18786 18972 19158 | 19344 19530 19716 19902 20088 20274 20460 20646 | 20832 21018 21204 21390 21576 21762 21948 22134 | 22320 22506 22692 22878 23064 23250 23558 | Running AMBER/MPI version on 126 nodes Sum of charges from parm topology file = -11.00000006 Forcing neutrality... --------------------------------------------------- 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 = 0.2088E-14 at 2.598900 | CHECK d/dx switch(x): max rel err = 0.7671E-11 at 2.757160 --------------------------------------------------- Total number of mask terms = 34709 Total number of mask terms = 69418 | Total Ewald setup time = 0.28572750 ------------------------------------------------------------------------------ NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 436.89 PRESS = 0.00 Etot = -45424.6591 EKtot = 21002.9065 EPtot = -66427.5656 BOND = 98.5019 ANGLE = 410.5387 DIHED = 805.7590 1-4 NB = 614.1164 1-4 EEL = 7104.4424 VDWAALS = 4790.9648 EELEC = -80251.8887 EHBOND = 0.0000 CONSTRAINT = 0.0000 Ewald error estimate: 0.1425E-02 ------------------------------------------------------------------------------ NSTEP = 100 TIME(PS) = 0.100 TEMP(K) = 341.94 PRESS = 0.00 Etot = -52070.7160 EKtot = 16438.2467 EPtot = -68508.9627 BOND = 424.6502 ANGLE = 1145.5619 DIHED = 1030.9361 1-4 NB = 533.8425 1-4 EEL = 6477.1604 VDWAALS = 8251.7818 EELEC = -86372.8957 EHBOND = 0.0000 CONSTRAINT = 0.0000 Ewald error estimate: 0.2890E-03 ------------------------------------------------------------------------------ NSTEP = 200 TIME(PS) = 0.200 TEMP(K) = 342.89 PRESS = 0.00 Etot = -52070.7614 EKtot = 16484.2530 EPtot = -68555.0144 BOND = 361.6936 ANGLE = 1146.3981 DIHED = 1045.0411 1-4 NB = 566.2224 1-4 EEL = 6564.9541 VDWAALS = 8047.9505 EELEC = -86287.2742 EHBOND = 0.0000 CONSTRAINT = 0.0000 Ewald error estimate: 0.3991E-04 ------------------------------------------------------------------------------ NSTEP = 300 TIME(PS) = 0.300 TEMP(K) = 339.45 PRESS = 0.00 Etot = -52071.0780 EKtot = 16318.7018 EPtot = -68389.7798 BOND = 370.7418 ANGLE = 1132.3021 DIHED = 1063.8323 1-4 NB = 547.3142 1-4 EEL = 6549.3791 VDWAALS = 7698.6647 EELEC = -85752.0141 EHBOND = 0.0000 CONSTRAINT = 0.0000 Ewald error estimate: 0.8891E-04 ------------------------------------------------------------------------------ NSTEP = 400 TIME(PS) = 0.400 TEMP(K) = 339.83 PRESS = 0.00 Etot = -52071.6976 EKtot = 16337.0121 EPtot = -68408.7097 BOND = 388.1232 ANGLE = 1145.1296 DIHED = 1027.5420 1-4 NB = 560.6767 1-4 EEL = 6597.0788 VDWAALS = 7791.9710 EELEC = -85919.2310 EHBOND = 0.0000 CONSTRAINT = 0.0000 Ewald error estimate: 0.2532E-04 ------------------------------------------------------------------------------ NSTEP = 500 TIME(PS) = 0.500 TEMP(K) = 340.83 PRESS = 0.00 Etot = -52070.5632 EKtot = 16385.3016 EPtot = -68455.8647 BOND = 415.5202 ANGLE = 1186.8791 DIHED = 1014.8376 1-4 NB = 551.1868 1-4 EEL = 6547.1283 VDWAALS = 7569.0142 EELEC = -85740.4309 EHBOND = 0.0000 CONSTRAINT = 0.0000 Ewald error estimate: 0.4445E-04 ------------------------------------------------------------------------------ A V E R A G E S O V E R 500 S T E P S NSTEP = 500 TIME(PS) = 0.500 TEMP(K) = 339.13 PRESS = 0.00 Etot = -52057.9046 EKtot = 16303.3183 EPtot = -68361.2229 BOND = 378.8697 ANGLE = 1118.0702 DIHED = 1038.3148 1-4 NB = 556.9583 1-4 EEL = 6581.3192 VDWAALS = 7537.2669 EELEC = -85572.0220 EHBOND = 0.0000 CONSTRAINT = 0.0000 Ewald error estimate: 0.1715E-03 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 500 TIME(PS) = 0.500 TEMP(K) = 8.99 PRESS = 0.00 Etot = 297.1036 EKtot = 432.0046 EPtot = 388.8519 BOND = 35.3622 ANGLE = 70.9069 DIHED = 28.4969 1-4 NB = 27.5367 1-4 EEL = 83.8194 VDWAALS = 890.8266 EELEC = 1253.1135 EHBOND = 0.0000 CONSTRAINT = 0.0000 Ewald error estimate: 0.2284E-03 ------------------------------------------------------------------------------ | | ELAPSED TIME = 190.180 TOTAL TIME = 190.180 | Nonbond Ewald pairlist time components: | map, save_t = 0.53 0.28 | grid setup_t = 0.00 0.00 | grid ucell_t = 0.13 0.07 | grid image_t = 0.03 0.02 | build list_t = 0.88 0.46 | total list_t = 1.57 0.82 Nonbond Ewald force time components: | zero ene,force = 0.45 0.24 | map = 0.00 0.00 | map,adjust = 2.74 1.44 | self energy = 0.01 0.00 | 1-dim b-spline= 1.99 1.04 | grid charges = 1.59 0.83 | scalar sum = 1.13 0.60 | grad sum = 2.62 1.38 | FFT = 47.96 25.22 | Recip force = 55.29 29.07 | Direct force = 9.11 4.79 | adjust masked = 0.60 0.31 | accum force = 1.17 0.61 | finish virial = 4.17 2.19 | mfct4 = 0.65 0.34 | f_wait = 4.13 2.17 | stack_time = 0.07 0.04 | total force = 78.37 41.21 | | Routine Sec % | ---------------------------- | Nonbond 88.17 46.36 | Bond 0.05 0.03 | Angle 0.43 0.22 | Dihedral 0.82 0.43 | Shake 1.65 0.87 | GBrad 0.00 0.00 | Force 0.00 0.00 | GBraddist 0.00 0.00 | F,Xdist 74.12 38.97 | Other 15.17 7.98 | ---------------------------- | Total 190.18 0.05 Hours | Nonsetup 176.75 92.94% | Highest rstack allocated: 70674 | MAX_RSTACK = 10000000 | Highest istack allocated: 1963 | MAX_ISTACK = 200000 | Setup wallclock 19 seconds | Nonsetup wallclock 182 seconds