------------------------------------------------------- Amber 14 SANDER 2014 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 11 | Run on 06/21/2011 at 15:35:07 | 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: myoglobin_md_igb7.out | INPCRD: inpcrd | PARM: prmtop.igb78 | RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo Here is the input file: Myoglobin MD &cntrl imin=0,irest=1,ntx=5, nstlim=20,dt=0.002,ntb=0, ntf=2,ntc=2,tol=0.000001, ntpr=1, ntwx=0, ntwr=25, cut=9999.0, rgbmax=15.0, igb=7,ntt=0,nscm=0, / | Conditional Compilation Defines Used: | DIRFRC_COMTRANS | DIRFRC_EFS | DIRFRC_NOVEC | PUBFFT | FFTLOADBAL_2PROC | BINTRAJ | MKL | New format PARM file being parsed. | Version = 1.000 Date = 09/17/01 Time = 12:09:08 | 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: -------------------------------------------------------------------------------- NATOM = 2492 NTYPES = 14 NBONH = 1275 MBONA = 1245 NTHETH = 2900 MTHETA = 1673 NPHIH = 5168 MPHIA = 2923 NHPARM = 0 NPARM = 0 NNB = 13801 NRES = 153 NBONA = 1245 NTHETA = 1673 NPHIA = 2923 NUMBND = 38 NUMANG = 88 NPTRA = 31 NATYP = 25 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Replacing prmtop screening parameters with GBn (igb=7) values -------------------------------------------------------------------------------- 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 = 25 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 0, igb = 7, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut =9999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.09511 gbbeta = 1.90793, gbgamma = 2.50798, surften = 0.00500 rdt = 0.00000, rgbmax = 15.00000 extdiel = 78.50000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 20, nscm = 0, nrespa = 1 t = 0.00000, dt = 0.00200, 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 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 1.500 ps Number of triangulated 3-point waters found: 0 | Dynamic Memory, Types Used: | Reals 76745 | Integers 227326 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NSTEP = 1 TIME(PS) = 1.502 TEMP(K) = 305.34 PRESS = 0.0 Etot = -819.2397 EKtot = 1881.3075 EPtot = -2700.5472 BOND = 446.2716 ANGLE = 1444.5851 DIHED = 800.1506 1-4 NB = 526.9513 1-4 EEL = 7881.6446 VDWAALS = -1151.3755 EELEC = -382.5872 EGB = -12266.1876 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 2 TIME(PS) = 1.504 TEMP(K) = 324.93 PRESS = 0.0 Etot = -827.9209 EKtot = 2001.9659 EPtot = -2829.8867 BOND = 422.7090 ANGLE = 1363.7046 DIHED = 796.3460 1-4 NB = 522.7309 1-4 EEL = 7882.9502 VDWAALS = -1158.8738 EELEC = -393.2813 EGB = -12266.1721 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 3 TIME(PS) = 1.506 TEMP(K) = 321.71 PRESS = 0.0 Etot = -825.1755 EKtot = 1982.1181 EPtot = -2807.2936 BOND = 439.6249 ANGLE = 1392.6436 DIHED = 795.4684 1-4 NB = 521.0423 1-4 EEL = 7877.9520 VDWAALS = -1164.0700 EELEC = -400.8319 EGB = -12269.1229 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 4 TIME(PS) = 1.508 TEMP(K) = 301.34 PRESS = 0.0 Etot = -814.8118 EKtot = 1856.6481 EPtot = -2671.4599 BOND = 477.9667 ANGLE = 1505.4473 DIHED = 798.3709 1-4 NB = 522.3138 1-4 EEL = 7867.6872 VDWAALS = -1165.4283 EELEC = -404.2340 EGB = -12273.5835 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 5 TIME(PS) = 1.510 TEMP(K) = 286.43 PRESS = 0.0 Etot = -808.7370 EKtot = 1764.7594 EPtot = -2573.4964 BOND = 496.5916 ANGLE = 1594.7609 DIHED = 803.8983 1-4 NB = 523.6824 1-4 EEL = 7854.1284 VDWAALS = -1164.6376 EELEC = -404.1744 EGB = -12277.7460 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 6 TIME(PS) = 1.512 TEMP(K) = 290.54 PRESS = 0.0 Etot = -812.9937 EKtot = 1790.0711 EPtot = -2603.0647 BOND = 482.5042 ANGLE = 1588.5372 DIHED = 810.3138 1-4 NB = 522.5183 1-4 EEL = 7839.6961 VDWAALS = -1163.9480 EELEC = -401.9651 EGB = -12280.7214 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 7 TIME(PS) = 1.514 TEMP(K) = 304.74 PRESS = 0.0 Etot = -821.5189 EKtot = 1877.6149 EPtot = -2699.1338 BOND = 460.9364 ANGLE = 1520.5563 DIHED = 816.8635 1-4 NB = 519.8283 1-4 EEL = 7826.8759 VDWAALS = -1163.3655 EELEC = -398.6995 EGB = -12282.1292 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 8 TIME(PS) = 1.516 TEMP(K) = 310.80 PRESS = 0.0 Etot = -823.8382 EKtot = 1914.9496 EPtot = -2738.7877 BOND = 455.5794 ANGLE = 1483.1723 DIHED = 823.5662 1-4 NB = 518.4427 1-4 EEL = 7817.8583 VDWAALS = -1160.4012 EELEC = -395.3811 EGB = -12281.6245 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 9 TIME(PS) = 1.518 TEMP(K) = 303.45 PRESS = 0.0 Etot = -818.3176 EKtot = 1869.6169 EPtot = -2687.9344 BOND = 457.7830 ANGLE = 1519.0067 DIHED = 830.0973 1-4 NB = 519.0970 1-4 EEL = 7814.0418 VDWAALS = -1155.6423 EELEC = -393.2649 EGB = -12279.0531 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 10 TIME(PS) = 1.520 TEMP(K) = 294.17 PRESS = 0.0 Etot = -813.0428 EKtot = 1812.4645 EPtot = -2625.5073 BOND = 447.0891 ANGLE = 1576.6419 DIHED = 835.4528 1-4 NB = 520.3865 1-4 EEL = 7815.5325 VDWAALS = -1152.3478 EELEC = -393.5616 EGB = -12274.7006 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 11 TIME(PS) = 1.522 TEMP(K) = 294.44 PRESS = 0.0 Etot = -814.1068 EKtot = 1814.1336 EPtot = -2628.2404 BOND = 428.0616 ANGLE = 1580.2851 DIHED = 838.8299 1-4 NB = 521.4158 1-4 EEL = 7820.9967 VDWAALS = -1151.5734 EELEC = -396.7474 EGB = -12269.5087 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 12 TIME(PS) = 1.524 TEMP(K) = 302.38 PRESS = 0.0 Etot = -818.7344 EKtot = 1863.0665 EPtot = -2681.8009 BOND = 425.3211 ANGLE = 1521.4661 DIHED = 840.4454 1-4 NB = 522.4190 1-4 EEL = 7828.1446 VDWAALS = -1152.6957 EELEC = -402.1163 EGB = -12264.7851 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 13 TIME(PS) = 1.526 TEMP(K) = 307.93 PRESS = 0.0 Etot = -821.1645 EKtot = 1897.2472 EPtot = -2718.4116 BOND = 445.1036 ANGLE = 1462.8197 DIHED = 841.4285 1-4 NB = 523.3737 1-4 EEL = 7834.6451 VDWAALS = -1155.5724 EELEC = -408.2393 EGB = -12261.9705 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 14 TIME(PS) = 1.528 TEMP(K) = 305.37 PRESS = 0.0 Etot = -819.7276 EKtot = 1881.4710 EPtot = -2701.1986 BOND = 463.8483 ANGLE = 1463.8892 DIHED = 843.0849 1-4 NB = 523.9233 1-4 EEL = 7838.9364 VDWAALS = -1159.6448 EELEC = -413.8987 EGB = -12261.3372 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 15 TIME(PS) = 1.530 TEMP(K) = 297.51 PRESS = 0.0 Etot = -816.8204 EKtot = 1833.0551 EPtot = -2649.8756 BOND = 461.2298 ANGLE = 1522.3490 DIHED = 845.7353 1-4 NB = 524.0822 1-4 EEL = 7840.5052 VDWAALS = -1163.0705 EELEC = -418.5226 EGB = -12262.1839 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 16 TIME(PS) = 1.532 TEMP(K) = 291.10 PRESS = 0.0 Etot = -814.6842 EKtot = 1793.5533 EPtot = -2608.2375 BOND = 447.2996 ANGLE = 1582.8445 DIHED = 848.2037 1-4 NB = 523.5252 1-4 EEL = 7839.7321 VDWAALS = -1164.7188 EELEC = -422.0700 EGB = -12263.0539 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 17 TIME(PS) = 1.534 TEMP(K) = 291.08 PRESS = 0.0 Etot = -814.7731 EKtot = 1793.4438 EPtot = -2608.2169 BOND = 445.6451 ANGLE = 1591.7292 DIHED = 848.8425 1-4 NB = 521.2299 1-4 EEL = 7837.5516 VDWAALS = -1165.5174 EELEC = -424.7840 EGB = -12262.9136 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 18 TIME(PS) = 1.536 TEMP(K) = 297.06 PRESS = 0.0 Etot = -817.3070 EKtot = 1830.2715 EPtot = -2647.5785 BOND = 460.4734 ANGLE = 1547.4609 DIHED = 847.4378 1-4 NB = 516.9872 1-4 EEL = 7835.0948 VDWAALS = -1166.5314 EELEC = -426.9797 EGB = -12261.5214 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 19 TIME(PS) = 1.538 TEMP(K) = 303.31 PRESS = 0.0 Etot = -820.1405 EKtot = 1868.8000 EPtot = -2688.9405 BOND = 474.1812 ANGLE = 1500.5572 DIHED = 845.7189 1-4 NB = 512.8292 1-4 EEL = 7833.2661 VDWAALS = -1167.2005 EELEC = -428.8647 EGB = -12259.4279 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 20 TIME(PS) = 1.540 TEMP(K) = 303.66 PRESS = 0.0 Etot = -820.4753 EKtot = 1870.9064 EPtot = -2691.3817 BOND = 474.7742 ANGLE = 1499.3323 DIHED = 845.5093 1-4 NB = 511.2024 1-4 EEL = 7832.3409 VDWAALS = -1166.8937 EELEC = -430.2438 EGB = -12257.4034 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ A V E R A G E S O V E R 20 S T E P S NSTEP = 20 TIME(PS) = 1.540 TEMP(K) = 301.86 PRESS = 0.0 Etot = -818.1765 EKtot = 1859.8732 EPtot = -2678.0497 BOND = 455.6497 ANGLE = 1513.0895 DIHED = 827.7882 1-4 NB = 520.8991 1-4 EEL = 7840.9790 VDWAALS = -1160.6754 EELEC = -407.0224 EGB = -12268.7573 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 20 TIME(PS) = 1.540 TEMP(K) = 9.59 PRESS = 0.0 Etot = 4.5038 EKtot = 59.0709 EPtot = 63.3574 BOND = 19.0050 ANGLE = 63.7017 DIHED = 19.5522 1-4 NB = 3.6912 1-4 EEL = 20.6970 VDWAALS = 5.4173 EELEC = 13.6164 EGB = 7.8804 RESTRAINT = 0.0000 |E(PBS) = 0.2958 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 5.25 99.09 | Bond 0.00 0.02 | Angle 0.01 0.15 | Dihedral 0.02 0.45 | Shake 0.00 0.06 | RunMD 0.01 0.23 | Other 0.00 0.00 | ------------------------------ | Total 5.29 | Generalized Born CPU Time: | | Routine Sec % | ------------------------------------ | Radii Calc 0.96 18.21 | Diagonal Calc 1.68 31.73 | Off Diagonal Calc 2.60 49.04 | GBSA LCPO Calc 0.00 0.00 | --------------------------------- | Total 5.24 98.98 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 19 steps: | Elapsed(s) = 5.10 Per Step(ms) = 268.33 | ns/day = 0.64 seconds/ns = 134165.92 | | Average timings for all steps: | Elapsed(s) = 5.44 Per Step(ms) = 271.75 | ns/day = 0.64 seconds/ns = 135875.47 | ----------------------------------------------------- | Setup CPU time: 0.02 seconds | NonSetup CPU time: 5.29 seconds | Total CPU time: 5.32 seconds 0.00 hours | Setup wall time: 0 seconds | NonSetup wall time: 6 seconds | Total wall time: 6 seconds 0.00 hours