------------------------------------------------------- Amber 12 SANDER 2012 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 11 | Run on 06/21/2011 at 09:22:48 | WARNING: Stack usage limited by a hard resource limit of 536870912 bytes! | If segment violations occur, get your sysadmin to increase the limit. [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: mdout.dhfr.ntr1.CPU | INPCRD: md12.x | PARM: prmtop | RESTRT: restrt | REFC: md12.x | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo Here is the input file: short md, nve ensemble &cntrl ntx=7, irest=1, ntc=2, ntf=2, tol=0.0000001, nstlim=20, ntt=0, ntpr=1, ntwr=10000, dt=0.001,ntr=1, / &ewald nfft1 = 72, nfft2 = 60, nfft3 = 60, / restraints 1 25.0 RES 2 5 END restraints 2 20.0 RES 9 11 END restraints 3 11.5 RES 50 50 END restrains 4 97.1 RES 17 22 END END | Conditional Compilation Defines Used: | DIRFRC_COMTRANS | DIRFRC_EFS | DIRFRC_NOVEC | PUBFFT | FFTLOADBAL_2PROC | BINTRAJ | MKL | Largest sphere to fit in unit cell has radius = 27.261 | INFO: Old style PARM file read | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting new box info from bottom of inpcrd NATOM = 22930 NTYPES = 17 NBONH = 21651 MBONA = 1302 NTHETH = 2789 MTHETA = 1772 NPHIH = 5026 MPHIA = 3140 NHPARM = 0 NPARM = 0 NNB = 41018 NRES = 6980 NBONA = 1302 NTHETA = 1772 NPHIA = 3140 NUMBND = 45 NUMANG = 91 NPTRA = 33 NATYP = 32 NPHB = 1 IFBOX = 1 NMXRS = 25 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 15 13 12 | Direct force subcell size = 4.6709 4.6571 4.5436 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 7, irest = 1, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 10000 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, 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 = 1 restraint_wt = 0.00000 Molecular dynamics: nstlim = 20, nscm = 0, 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 = 70.063 Box Y = 60.543 Box Z = 54.523 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 72 NFFT2 = 60 NFFT3 = 60 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES ----- READING GROUP 1; TITLE: restraints 1 GROUP 1 HAS HARMONIC CONSTRAINTS 25.00000 GRP 1 RES 2 TO 5 Number of atoms in this group = 68 ----- READING GROUP 2; TITLE: restraints 2 GROUP 2 HAS HARMONIC CONSTRAINTS 20.00000 GRP 2 RES 9 TO 11 Number of atoms in this group = 38 ----- READING GROUP 3; TITLE: restraints 3 GROUP 3 HAS HARMONIC CONSTRAINTS 11.50000 GRP 3 RES 50 TO 50 Number of atoms in this group = 19 ----- READING GROUP 4; TITLE: restrains 4 GROUP 4 HAS HARMONIC CONSTRAINTS 97.10000 GRP 4 RES 17 TO 22 Number of atoms in this group = 94 ----- END OF GROUP READ ----- -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 510.050 ps Number of triangulated 3-point waters found: 6810 Sum of charges from parm topology file = -0.00000006 Forcing neutrality... | Dynamic Memory, Types Used: | Reals 789971 | Integers 721716 | Nonbonded Pairs Initial Allocation: 3829883 -------------------------------------------------------------------------------- 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 = 1 TIME(PS) = 510.051 TEMP(K) = 301.27 PRESS = 0.0 Etot = -57751.7789 EKtot = 14110.5277 EPtot = -71862.3066 BOND = 452.1690 ANGLE = 1277.0334 DIHED = 968.3542 1-4 NB = 545.9440 1-4 EEL = 6666.3920 VDWAALS = 8109.3892 EELEC = -89881.5885 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.3682E-04 ------------------------------------------------------------------------------ NSTEP = 2 TIME(PS) = 510.052 TEMP(K) = 301.07 PRESS = 0.0 Etot = -57751.6597 EKtot = 14101.1958 EPtot = -71852.8555 BOND = 454.7406 ANGLE = 1280.2592 DIHED = 969.1508 1-4 NB = 547.4649 1-4 EEL = 6661.7831 VDWAALS = 8112.2872 EELEC = -89882.0013 EHBOND = 0.0000 RESTRAINT = 3.4599 EAMBER (non-restraint) = -71856.3154 Ewald error estimate: 0.2606E-04 ------------------------------------------------------------------------------ NSTEP = 3 TIME(PS) = 510.053 TEMP(K) = 300.65 PRESS = 0.0 Etot = -57751.4195 EKtot = 14081.5989 EPtot = -71833.0183 BOND = 459.7039 ANGLE = 1283.6600 DIHED = 971.0906 1-4 NB = 549.0167 1-4 EEL = 6656.3772 VDWAALS = 8116.0164 EELEC = -89881.4867 EHBOND = 0.0000 RESTRAINT = 12.6034 EAMBER (non-restraint) = -71845.6217 Ewald error estimate: 0.3634E-04 ------------------------------------------------------------------------------ NSTEP = 4 TIME(PS) = 510.054 TEMP(K) = 300.10 PRESS = 0.0 Etot = -57751.2357 EKtot = 14055.6878 EPtot = -71806.9235 BOND = 466.3748 ANGLE = 1286.2061 DIHED = 973.8765 1-4 NB = 550.3741 1-4 EEL = 6650.3700 VDWAALS = 8120.3119 EELEC = -89878.9387 EHBOND = 0.0000 RESTRAINT = 24.5018 EAMBER (non-restraint) = -71831.4253 Ewald error estimate: 0.6392E-04 ------------------------------------------------------------------------------ NSTEP = 5 TIME(PS) = 510.055 TEMP(K) = 299.52 PRESS = 0.0 Etot = -57750.9866 EKtot = 14028.4263 EPtot = -71779.4129 BOND = 473.7747 ANGLE = 1286.8945 DIHED = 977.0530 1-4 NB = 551.2870 1-4 EEL = 6643.9830 VDWAALS = 8124.9180 EELEC = -89873.2615 EHBOND = 0.0000 RESTRAINT = 35.9384 EAMBER (non-restraint) = -71815.3513 Ewald error estimate: 0.5337E-04 ------------------------------------------------------------------------------ NSTEP = 6 TIME(PS) = 510.056 TEMP(K) = 298.99 PRESS = 0.0 Etot = -57750.8727 EKtot = 14003.6867 EPtot = -71754.5595 BOND = 480.7846 ANGLE = 1285.2955 DIHED = 980.1270 1-4 NB = 551.5618 1-4 EEL = 6637.4444 VDWAALS = 8129.9230 EELEC = -89864.4664 EHBOND = 0.0000 RESTRAINT = 44.7705 EAMBER (non-restraint) = -71799.3300 Ewald error estimate: 0.7296E-04 ------------------------------------------------------------------------------ NSTEP = 7 TIME(PS) = 510.057 TEMP(K) = 298.55 PRESS = 0.0 Etot = -57750.9050 EKtot = 13983.0875 EPtot = -71733.9925 BOND = 486.3322 ANGLE = 1281.7099 DIHED = 982.6798 1-4 NB = 551.1204 1-4 EEL = 6630.9657 VDWAALS = 8135.0468 EELEC = -89852.4914 EHBOND = 0.0000 RESTRAINT = 50.6442 EAMBER (non-restraint) = -71784.6367 Ewald error estimate: 0.8569E-04 ------------------------------------------------------------------------------ NSTEP = 8 TIME(PS) = 510.058 TEMP(K) = 298.19 PRESS = 0.0 Etot = -57751.0970 EKtot = 13966.1959 EPtot = -71717.2928 BOND = 489.5913 ANGLE = 1276.9210 DIHED = 984.4303 1-4 NB = 550.0047 1-4 EEL = 6624.7221 VDWAALS = 8140.4107 EELEC = -89838.1354 EHBOND = 0.0000 RESTRAINT = 54.7625 EAMBER (non-restraint) = -71772.0553 Ewald error estimate: 0.1217E-03 ------------------------------------------------------------------------------ NSTEP = 9 TIME(PS) = 510.059 TEMP(K) = 297.88 PRESS = 0.0 Etot = -57751.2704 EKtot = 13951.6880 EPtot = -71702.9584 BOND = 490.1682 ANGLE = 1271.7745 DIHED = 985.2422 1-4 NB = 548.3369 1-4 EEL = 6618.8433 VDWAALS = 8146.0053 EELEC = -89822.2412 EHBOND = 0.0000 RESTRAINT = 58.9123 EAMBER (non-restraint) = -71761.8707 Ewald error estimate: 0.1425E-03 ------------------------------------------------------------------------------ NSTEP = 10 TIME(PS) = 510.060 TEMP(K) = 297.60 PRESS = 0.0 Etot = -57751.3434 EKtot = 13938.6520 EPtot = -71689.9954 BOND = 488.2257 ANGLE = 1266.8590 DIHED = 985.0958 1-4 NB = 546.2752 1-4 EEL = 6613.4165 VDWAALS = 8151.9767 EELEC = -89806.1533 EHBOND = 0.0000 RESTRAINT = 64.3092 EAMBER (non-restraint) = -71754.3046 Ewald error estimate: 0.1474E-03 ------------------------------------------------------------------------------ NSTEP = 11 TIME(PS) = 510.061 TEMP(K) = 297.36 PRESS = 0.0 Etot = -57751.2817 EKtot = 13927.3210 EPtot = -71678.6027 BOND = 484.4900 ANGLE = 1262.4313 DIHED = 984.0548 1-4 NB = 543.9831 1-4 EEL = 6608.4988 VDWAALS = 8158.4699 EELEC = -89791.3983 EHBOND = 0.0000 RESTRAINT = 70.8677 EAMBER (non-restraint) = -71749.4705 Ewald error estimate: 0.1430E-03 ------------------------------------------------------------------------------ NSTEP = 12 TIME(PS) = 510.062 TEMP(K) = 297.18 PRESS = 0.0 Etot = -57751.2828 EKtot = 13918.9060 EPtot = -71670.1888 BOND = 480.0992 ANGLE = 1258.5678 DIHED = 982.2454 1-4 NB = 541.6173 1-4 EEL = 6604.1364 VDWAALS = 8165.4623 EELEC = -89779.5667 EHBOND = 0.0000 RESTRAINT = 77.2495 EAMBER (non-restraint) = -71747.4383 Ewald error estimate: 0.1509E-03 ------------------------------------------------------------------------------ NSTEP = 13 TIME(PS) = 510.063 TEMP(K) = 297.09 PRESS = 0.0 Etot = -57751.2092 EKtot = 13914.7423 EPtot = -71665.9514 BOND = 476.3009 ANGLE = 1255.4246 DIHED = 979.8452 1-4 NB = 539.3245 1-4 EEL = 6600.3836 VDWAALS = 8172.9611 EELEC = -89771.8055 EHBOND = 0.0000 RESTRAINT = 81.6142 EAMBER (non-restraint) = -71747.5657 Ewald error estimate: 0.1413E-03 ------------------------------------------------------------------------------ NSTEP = 14 TIME(PS) = 510.064 TEMP(K) = 297.10 PRESS = 0.0 Etot = -57751.1042 EKtot = 13915.2967 EPtot = -71666.4009 BOND = 474.0732 ANGLE = 1253.4390 DIHED = 977.0793 1-4 NB = 537.2422 1-4 EEL = 6597.3162 VDWAALS = 8180.9520 EELEC = -89769.1395 EHBOND = 0.0000 RESTRAINT = 82.6366 EAMBER (non-restraint) = -71749.0375 Ewald error estimate: 0.1170E-03 ------------------------------------------------------------------------------ NSTEP = 15 TIME(PS) = 510.065 TEMP(K) = 297.19 PRESS = 0.0 Etot = -57751.1562 EKtot = 13919.6668 EPtot = -71670.8230 BOND = 473.8016 ANGLE = 1253.3182 DIHED = 974.2245 1-4 NB = 535.4908 1-4 EEL = 6595.0340 VDWAALS = 8189.4088 EELEC = -89772.3340 EHBOND = 0.0000 RESTRAINT = 80.2330 EAMBER (non-restraint) = -71751.0560 Ewald error estimate: 0.1076E-03 ------------------------------------------------------------------------------ NSTEP = 16 TIME(PS) = 510.066 TEMP(K) = 297.33 PRESS = 0.0 Etot = -57751.2765 EKtot = 13925.9095 EPtot = -71677.1860 BOND = 475.1514 ANGLE = 1255.7614 DIHED = 971.6107 1-4 NB = 534.1508 1-4 EEL = 6593.6493 VDWAALS = 8198.2792 EELEC = -89781.4132 EHBOND = 0.0000 RESTRAINT = 75.6244 EAMBER (non-restraint) = -71752.8104 Ewald error estimate: 0.9766E-04 ------------------------------------------------------------------------------ NSTEP = 17 TIME(PS) = 510.067 TEMP(K) = 297.46 PRESS = 0.0 Etot = -57751.3933 EKtot = 13931.9940 EPtot = -71683.3874 BOND = 477.2174 ANGLE = 1261.0269 DIHED = 969.6001 1-4 NB = 533.2370 1-4 EEL = 6593.2632 VDWAALS = 8207.5148 EELEC = -89795.9789 EHBOND = 0.0000 RESTRAINT = 70.7321 EAMBER (non-restraint) = -71754.1195 Ewald error estimate: 0.9259E-04 ------------------------------------------------------------------------------ NSTEP = 18 TIME(PS) = 510.068 TEMP(K) = 297.56 PRESS = 0.0 Etot = -57751.5100 EKtot = 13936.8178 EPtot = -71688.3278 BOND = 478.9159 ANGLE = 1268.5842 DIHED = 968.5303 1-4 NB = 532.6876 1-4 EEL = 6593.9378 VDWAALS = 8216.8316 EELEC = -89815.0728 EHBOND = 0.0000 RESTRAINT = 67.2577 EAMBER (non-restraint) = -71755.5855 Ewald error estimate: 0.9152E-04 ------------------------------------------------------------------------------ NSTEP = 19 TIME(PS) = 510.069 TEMP(K) = 297.64 PRESS = 0.0 Etot = -57751.4512 EKtot = 13940.6768 EPtot = -71692.1280 BOND = 479.4616 ANGLE = 1277.0768 DIHED = 968.6303 1-4 NB = 532.3782 1-4 EEL = 6595.6737 VDWAALS = 8226.0902 EELEC = -89837.3919 EHBOND = 0.0000 RESTRAINT = 65.9530 EAMBER (non-restraint) = -71758.0810 Ewald error estimate: 0.1105E-03 ------------------------------------------------------------------------------ NSTEP = 20 TIME(PS) = 510.070 TEMP(K) = 297.73 PRESS = 0.0 Etot = -57751.2620 EKtot = 13944.9045 EPtot = -71696.1665 BOND = 478.7213 ANGLE = 1284.6639 DIHED = 969.9447 1-4 NB = 532.1538 1-4 EEL = 6598.4003 VDWAALS = 8234.4559 EELEC = -89860.9581 EHBOND = 0.0000 RESTRAINT = 66.4517 EAMBER (non-restraint) = -71762.6182 Ewald error estimate: 0.9374E-04 ------------------------------------------------------------------------------ A V E R A G E S O V E R 20 S T E P S NSTEP = 20 TIME(PS) = 510.070 TEMP(K) = 298.37 PRESS = 0.0 Etot = -57751.2748 EKtot = 13974.8491 EPtot = -71726.1239 BOND = 476.0049 ANGLE = 1271.3454 DIHED = 976.1433 1-4 NB = 542.6826 1-4 EEL = 6619.2295 VDWAALS = 8161.8355 EELEC = -89827.7912 EHBOND = 0.0000 RESTRAINT = 54.4261 EAMBER (non-restraint) = -71780.5500 Ewald error estimate: 0.9663E-04 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 20 TIME(PS) = 510.070 TEMP(K) = 1.36 PRESS = 0.0 Etot = 0.2226 EKtot = 63.7689 EPtot = 63.8465 BOND = 10.4289 ANGLE = 11.8079 DIHED = 6.1868 1-4 NB = 7.1754 1-4 EEL = 24.7507 VDWAALS = 38.7625 EELEC = 41.0961 EHBOND = 0.0000 RESTRAINT = 25.4178 EAMBER (non-restraint) = 38.4287 |E(PBS) = 0.1826 Ewald error estimate: 0.3807E-04 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 2.61 90.66 | Bond 0.00 0.00 | Angle 0.02 0.69 | Dihedral 0.04 1.46 | Shake 0.03 1.08 | RunMD 0.18 6.11 | Other 0.00 0.00 | ------------------------------ | Total 2.88 | PME Nonbond Pairlist CPU Time: | | Routine Sec % | --------------------------------- | Set Up Cit 0.00 0.14 | Build List 0.27 9.38 | --------------------------------- | Total 0.27 9.51 | PME Direct Force CPU Time: | | Routine Sec % | --------------------------------- | NonBonded Calc 1.83 63.44 | Exclude Masked 0.04 1.39 | Other 0.01 0.31 | --------------------------------- | Total 1.88 65.14 | PME Reciprocal Force CPU Time: | | Routine Sec % | --------------------------------- | 1D bspline 0.03 1.18 | Grid Charges 0.05 1.77 | Scalar Sum 0.08 2.78 | Gradient Sum 0.07 2.40 | FFT 0.23 7.88 | --------------------------------- | Total 0.46 16.01 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 19 steps: | Elapsed(s) = 2.72 Per Step(ms) = 143.30 | ns/day = 0.60 seconds/ns = 143303.48 | | Average timings for all steps: | Elapsed(s) = 2.99 Per Step(ms) = 149.34 | ns/day = 0.58 seconds/ns = 149335.80 | ----------------------------------------------------- | Setup CPU time: 0.25 seconds | NonSetup CPU time: 2.88 seconds | Total CPU time: 3.13 seconds 0.00 hours | Setup wall time: 0 seconds | NonSetup wall time: 3 seconds | Total wall time: 3 seconds 0.00 hours