------------------------------------------------------- Amber 14 SANDER 2014 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 11 | Run on 06/21/2011 at 15:41:21 | 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_igb8.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=8,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 GBn2 (igb=8) 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 = 8, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut =9999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.19514, surften = 0.00500 rdt = 0.00000, rgbmax = 15.00000 extdiel = 78.50000 alpb = 0 gbalphaH = 0.78844, gbbetaH = 0.79870, gbgammaH = 0.43733 gbalphaC = 0.73376, gbbetaC = 0.50638, gbgammaC = 0.20584 gbalphaN = 0.50336, gbbetaN = 0.31683, gbgammaN = 0.19292 gbalphaOS = 0.86781, gbbetaOS = 0.87664, gbgammaOS = 0.38788 gbalphaP = 1.00000, gbbetaP = 0.80000, gbgammaP = 4.85100 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) = 305.28 PRESS = 0.0 Etot = -1169.5941 EKtot = 1880.9096 EPtot = -3050.5037 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 = -12616.1441 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 2 TIME(PS) = 1.504 TEMP(K) = 324.33 PRESS = 0.0 Etot = -1178.1236 EKtot = 1998.3090 EPtot = -3176.4326 BOND = 422.0373 ANGLE = 1364.5434 DIHED = 796.0257 1-4 NB = 522.8543 1-4 EEL = 7884.7584 VDWAALS = -1158.4891 EELEC = -393.4534 EGB = -12614.7092 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 3 TIME(PS) = 1.506 TEMP(K) = 320.48 PRESS = 0.0 Etot = -1175.1744 EKtot = 1974.5490 EPtot = -3149.7234 BOND = 437.5632 ANGLE = 1393.8188 DIHED = 794.4009 1-4 NB = 521.3706 1-4 EEL = 7883.0168 VDWAALS = -1162.9856 EELEC = -401.5626 EGB = -12615.3455 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 4 TIME(PS) = 1.508 TEMP(K) = 299.84 PRESS = 0.0 Etot = -1164.7775 EKtot = 1847.3902 EPtot = -3012.1677 BOND = 473.9345 ANGLE = 1504.6544 DIHED = 796.0523 1-4 NB = 522.8630 1-4 EEL = 7876.8546 VDWAALS = -1163.4913 EELEC = -405.9706 EGB = -12617.0645 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 5 TIME(PS) = 1.510 TEMP(K) = 285.09 PRESS = 0.0 Etot = -1158.9152 EKtot = 1756.5426 EPtot = -2915.4578 BOND = 490.4629 ANGLE = 1589.6389 DIHED = 799.8346 1-4 NB = 524.4231 1-4 EEL = 7867.5451 VDWAALS = -1161.8731 EELEC = -407.2043 EGB = -12618.2850 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 6 TIME(PS) = 1.512 TEMP(K) = 289.43 PRESS = 0.0 Etot = -1163.3146 EKtot = 1783.2397 EPtot = -2946.5543 BOND = 474.7543 ANGLE = 1579.0933 DIHED = 804.1208 1-4 NB = 523.3964 1-4 EEL = 7856.9332 VDWAALS = -1160.5622 EELEC = -406.2875 EGB = -12618.0026 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 7 TIME(PS) = 1.514 TEMP(K) = 303.58 PRESS = 0.0 Etot = -1171.7743 EKtot = 1870.4341 EPtot = -3042.2084 BOND = 452.3389 ANGLE = 1509.2255 DIHED = 808.3025 1-4 NB = 520.8450 1-4 EEL = 7847.2281 VDWAALS = -1159.6767 EELEC = -404.1136 EGB = -12616.3582 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 8 TIME(PS) = 1.516 TEMP(K) = 309.38 PRESS = 0.0 Etot = -1173.9821 EKtot = 1906.1749 EPtot = -3080.1570 BOND = 446.7509 ANGLE = 1472.5014 DIHED = 812.5080 1-4 NB = 519.7558 1-4 EEL = 7840.6603 VDWAALS = -1156.6706 EELEC = -401.6622 EGB = -12614.0006 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 9 TIME(PS) = 1.518 TEMP(K) = 301.80 PRESS = 0.0 Etot = -1168.4327 EKtot = 1859.4822 EPtot = -3027.9149 BOND = 449.1467 ANGLE = 1510.0714 DIHED = 816.4988 1-4 NB = 521.0178 1-4 EEL = 7838.8605 VDWAALS = -1151.9515 EELEC = -400.2520 EGB = -12611.3065 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 10 TIME(PS) = 1.520 TEMP(K) = 292.39 PRESS = 0.0 Etot = -1163.2087 EKtot = 1801.4965 EPtot = -2964.7052 BOND = 439.1035 ANGLE = 1569.4240 DIHED = 819.4388 1-4 NB = 523.2740 1-4 EEL = 7842.1895 VDWAALS = -1148.6504 EELEC = -401.1815 EGB = -12608.3031 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 11 TIME(PS) = 1.522 TEMP(K) = 292.56 PRESS = 0.0 Etot = -1164.2212 EKtot = 1802.5598 EPtot = -2966.7811 BOND = 421.0510 ANGLE = 1574.1219 DIHED = 820.7752 1-4 NB = 525.6315 1-4 EEL = 7849.5093 VDWAALS = -1147.7940 EELEC = -405.0340 EGB = -12605.0421 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 12 TIME(PS) = 1.524 TEMP(K) = 300.50 PRESS = 0.0 Etot = -1168.8855 EKtot = 1851.4975 EPtot = -3020.3831 BOND = 419.0806 ANGLE = 1514.9634 DIHED = 820.9178 1-4 NB = 528.3173 1-4 EEL = 7858.5935 VDWAALS = -1148.7703 EELEC = -411.2559 EGB = -12602.2294 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 13 TIME(PS) = 1.526 TEMP(K) = 306.12 PRESS = 0.0 Etot = -1171.3646 EKtot = 1886.1144 EPtot = -3057.4791 BOND = 439.0128 ANGLE = 1454.6592 DIHED = 821.0723 1-4 NB = 531.2843 1-4 EEL = 7867.0317 VDWAALS = -1151.3687 EELEC = -418.5797 EGB = -12600.5909 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 14 TIME(PS) = 1.528 TEMP(K) = 303.52 PRESS = 0.0 Etot = -1169.9977 EKtot = 1870.0769 EPtot = -3040.0746 BOND = 457.4128 ANGLE = 1453.7187 DIHED = 822.5161 1-4 NB = 534.1447 1-4 EEL = 7873.0631 VDWAALS = -1154.9845 EELEC = -425.8546 EGB = -12600.0909 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 15 TIME(PS) = 1.530 TEMP(K) = 295.42 PRESS = 0.0 Etot = -1166.9960 EKtot = 1820.1846 EPtot = -2987.1805 BOND = 454.3412 ANGLE = 1510.2583 DIHED = 825.4808 1-4 NB = 536.8054 1-4 EEL = 7875.9759 VDWAALS = -1157.8656 EELEC = -432.4126 EGB = -12599.7639 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 16 TIME(PS) = 1.532 TEMP(K) = 288.75 PRESS = 0.0 Etot = -1164.7775 EKtot = 1779.0643 EPtot = -2943.8418 BOND = 439.8158 ANGLE = 1568.3578 DIHED = 828.6567 1-4 NB = 538.6611 1-4 EEL = 7876.0934 VDWAALS = -1159.0170 EELEC = -438.0127 EGB = -12598.3968 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 17 TIME(PS) = 1.534 TEMP(K) = 288.62 PRESS = 0.0 Etot = -1164.8988 EKtot = 1778.2947 EPtot = -2943.1935 BOND = 436.7772 ANGLE = 1574.5171 DIHED = 830.2797 1-4 NB = 538.5027 1-4 EEL = 7874.5075 VDWAALS = -1159.4223 EELEC = -442.7505 EGB = -12595.6050 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 18 TIME(PS) = 1.536 TEMP(K) = 294.60 PRESS = 0.0 Etot = -1167.5050 EKtot = 1815.1198 EPtot = -2982.6248 BOND = 448.8129 ANGLE = 1528.6120 DIHED = 830.1143 1-4 NB = 536.0641 1-4 EEL = 7872.6712 VDWAALS = -1160.0962 EELEC = -446.9389 EGB = -12591.8642 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 19 TIME(PS) = 1.538 TEMP(K) = 300.81 PRESS = 0.0 Etot = -1170.3365 EKtot = 1853.3924 EPtot = -3023.7289 BOND = 458.5791 ANGLE = 1481.9050 DIHED = 829.9529 1-4 NB = 533.3693 1-4 EEL = 7871.8164 VDWAALS = -1160.4509 EELEC = -450.8794 EGB = -12588.0213 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 20 TIME(PS) = 1.540 TEMP(K) = 301.05 PRESS = 0.0 Etot = -1170.5992 EKtot = 1854.8839 EPtot = -3025.4832 BOND = 455.2904 ANGLE = 1481.5349 DIHED = 831.5754 1-4 NB = 532.9583 1-4 EEL = 7872.4245 VDWAALS = -1159.7969 EELEC = -454.4687 EGB = -12585.0011 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) = 300.18 PRESS = 0.0 Etot = -1168.3439 EKtot = 1849.4858 EPtot = -3017.8298 BOND = 448.1269 ANGLE = 1504.0102 DIHED = 815.4337 1-4 NB = 528.1245 1-4 EEL = 7865.5689 VDWAALS = -1156.7646 EELEC = -416.5231 EGB = -12605.8062 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) = 9.87 PRESS = 0.0 Etot = 4.5057 EKtot = 60.8056 EPtot = 65.0423 BOND = 17.6193 ANGLE = 60.9018 DIHED = 12.6487 1-4 NB = 6.3089 1-4 EEL = 14.4118 VDWAALS = 4.8881 EELEC = 20.3521 EGB = 10.3334 RESTRAINT = 0.0000 |E(PBS) = 0.2770 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 5.34 99.11 | Bond 0.00 0.00 | Angle 0.01 0.17 | Dihedral 0.03 0.48 | Shake 0.00 0.02 | RunMD 0.01 0.22 | Other 0.00 0.00 | ------------------------------ | Total 5.39 | Generalized Born CPU Time: | | Routine Sec % | ------------------------------------ | Radii Calc 1.02 18.99 | Diagonal Calc 1.76 32.68 | Off Diagonal Calc 2.55 47.36 | GBSA LCPO Calc 0.00 0.00 | --------------------------------- | Total 5.34 99.03 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 19 steps: | Elapsed(s) = 5.21 Per Step(ms) = 274.02 | ns/day = 0.63 seconds/ns = 137007.76 | | Average timings for all steps: | Elapsed(s) = 5.52 Per Step(ms) = 275.82 | ns/day = 0.63 seconds/ns = 137912.25 | ----------------------------------------------------- | Setup CPU time: 0.02 seconds | NonSetup CPU time: 5.39 seconds | Total CPU time: 5.41 seconds 0.00 hours | Setup wall time: 1 seconds | NonSetup wall time: 5 seconds | Total wall time: 6 seconds 0.00 hours