------------------------------------------------------- Amber 12 SANDER 2012 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 11 | Run on 04/14/2010 at 00:37:54 | 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: trpcage_md.out.CPU | INPCRD: inpcrd | PARM: prmtop | RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo Here is the input file: TRPCage MD &cntrl imin=0, irest=1, ntx=5, nstlim=20, dt=0.002, ntc=2, ntf=2, ntt=1, tautp=0.5, tempi=325.0, temp0=325.0, ntpr=1, ntwx=0,ntwr=100000, ntb=0, igb=1, cut=9999.,rgbmax=9999. / | Conditional Compilation Defines Used: | DIRFRC_COMTRANS | DIRFRC_EFS | DIRFRC_NOVEC | PUBFFT | FFTLOADBAL_2PROC | MKL | New format PARM file being parsed. | Version = 1.000 Date = 06/02/05 Time = 14:13:53 | 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 = 304 NTYPES = 12 NBONH = 150 MBONA = 160 NTHETH = 346 MTHETA = 219 NPHIH = 653 MPHIA = 403 NHPARM = 0 NPARM = 0 NNB = 1701 NRES = 20 NBONA = 160 NTHETA = 219 NPHIA = 403 NUMBND = 32 NUMANG = 70 NPTRA = 34 NATYP = 21 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- NASN 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 = 100000 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 0, igb = 1, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut =9999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500 rdt = 0.00000, rgbmax =9999.00000 extdiel = 78.50000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 20, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Berendsen (weak-coupling) temperature regulation: temp0 = 325.00000, tempi = 325.00000, tautp = 0.50000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 1 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- NASN begin time read from input coords = 50.000 ps Number of triangulated 3-point waters found: 0 | Dynamic Memory, Types Used: | Reals 8990 | Integers 28486 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NSTEP = 1 TIME(PS) = 50.002 TEMP(K) = 351.27 PRESS = 0.0 Etot = -219.1093 EKtot = 263.8622 EPtot = -482.9715 BOND = 57.2904 ANGLE = 152.0950 DIHED = 153.1874 1-4 NB = 57.2836 1-4 EEL = 886.3260 VDWAALS = -72.1725 EELEC = -1282.7867 EGB = -434.1947 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 2 TIME(PS) = 50.004 TEMP(K) = 361.20 PRESS = 0.0 Etot = -219.6009 EKtot = 271.3165 EPtot = -490.9175 BOND = 56.3048 ANGLE = 147.5455 DIHED = 151.8153 1-4 NB = 56.3806 1-4 EEL = 885.5111 VDWAALS = -72.3409 EELEC = -1282.8907 EGB = -433.2432 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 3 TIME(PS) = 50.006 TEMP(K) = 342.56 PRESS = 0.0 Etot = -218.4299 EKtot = 257.3161 EPtot = -475.7460 BOND = 62.5210 ANGLE = 156.5586 DIHED = 151.5438 1-4 NB = 56.4501 1-4 EEL = 885.0637 VDWAALS = -72.4533 EELEC = -1283.3986 EGB = -432.0313 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 4 TIME(PS) = 50.008 TEMP(K) = 317.73 PRESS = 0.0 Etot = -217.1552 EKtot = 238.6655 EPtot = -455.8207 BOND = 69.2004 ANGLE = 166.9339 DIHED = 153.2697 1-4 NB = 57.1613 1-4 EEL = 885.0897 VDWAALS = -72.0714 EELEC = -1284.8710 EGB = -430.5332 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 5 TIME(PS) = 50.010 TEMP(K) = 310.55 PRESS = 0.0 Etot = -217.2756 EKtot = 233.2697 EPtot = -450.5453 BOND = 70.0244 ANGLE = 166.4655 DIHED = 156.8407 1-4 NB = 57.9732 1-4 EEL = 885.4864 VDWAALS = -71.0600 EELEC = -1287.4175 EGB = -428.8579 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 6 TIME(PS) = 50.012 TEMP(K) = 319.15 PRESS = 0.0 Etot = -218.4047 EKtot = 239.7337 EPtot = -458.1385 BOND = 67.0959 ANGLE = 156.6628 DIHED = 161.0712 1-4 NB = 58.7854 1-4 EEL = 885.9351 VDWAALS = -69.9517 EELEC = -1290.4706 EGB = -427.2665 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 7 TIME(PS) = 50.014 TEMP(K) = 323.32 PRESS = 0.0 Etot = -218.9100 EKtot = 242.8618 EPtot = -461.7718 BOND = 67.0276 ANGLE = 149.6756 DIHED = 164.3611 1-4 NB = 59.7873 1-4 EEL = 886.1087 VDWAALS = -69.5483 EELEC = -1293.0731 EGB = -426.1107 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 8 TIME(PS) = 50.016 TEMP(K) = 313.92 PRESS = 0.0 Etot = -218.1306 EKtot = 235.8028 EPtot = -453.9334 BOND = 70.8441 ANGLE = 152.8524 DIHED = 165.4368 1-4 NB = 60.9760 1-4 EEL = 885.8954 VDWAALS = -69.8342 EELEC = -1294.4636 EGB = -425.6403 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 9 TIME(PS) = 50.018 TEMP(K) = 303.98 PRESS = 0.0 Etot = -217.2970 EKtot = 228.3390 EPtot = -445.6360 BOND = 72.7897 ANGLE = 160.3563 DIHED = 163.9466 1-4 NB = 62.1125 1-4 EEL = 885.4390 VDWAALS = -69.9942 EELEC = -1294.4095 EGB = -425.8763 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 10 TIME(PS) = 50.020 TEMP(K) = 307.11 PRESS = 0.0 Etot = -217.6220 EKtot = 230.6878 EPtot = -448.3098 BOND = 70.1632 ANGLE = 162.3446 DIHED = 160.7204 1-4 NB = 62.9387 1-4 EEL = 885.0086 VDWAALS = -69.6765 EELEC = -1293.1331 EGB = -426.6758 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 11 TIME(PS) = 50.022 TEMP(K) = 317.36 PRESS = 0.0 Etot = -218.3820 EKtot = 238.3862 EPtot = -456.7683 BOND = 68.4495 ANGLE = 157.4359 DIHED = 157.4049 1-4 NB = 63.2815 1-4 EEL = 884.8604 VDWAALS = -69.2850 EELEC = -1291.1553 EGB = -427.7601 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 12 TIME(PS) = 50.024 TEMP(K) = 321.21 PRESS = 0.0 Etot = -218.3143 EKtot = 241.2815 EPtot = -459.5959 BOND = 72.6304 ANGLE = 151.2050 DIHED = 155.5211 1-4 NB = 63.1154 1-4 EEL = 885.1861 VDWAALS = -69.2721 EELEC = -1289.2379 EGB = -428.7438 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 13 TIME(PS) = 50.026 TEMP(K) = 318.72 PRESS = 0.0 Etot = -217.7146 EKtot = 239.4129 EPtot = -457.1275 BOND = 78.3572 ANGLE = 147.1439 DIHED = 155.6504 1-4 NB = 62.7224 1-4 EEL = 886.1231 VDWAALS = -69.6698 EELEC = -1288.2649 EGB = -429.1897 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 14 TIME(PS) = 50.028 TEMP(K) = 319.23 PRESS = 0.0 Etot = -217.6735 EKtot = 239.7891 EPtot = -457.4626 BOND = 77.7590 ANGLE = 145.3355 DIHED = 157.2488 1-4 NB = 62.5190 1-4 EEL = 887.7444 VDWAALS = -70.3097 EELEC = -1288.9082 EGB = -428.8514 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 15 TIME(PS) = 50.030 TEMP(K) = 323.22 PRESS = 0.0 Etot = -218.1595 EKtot = 242.7880 EPtot = -460.9475 BOND = 71.0653 ANGLE = 146.3847 DIHED = 159.1299 1-4 NB = 62.5573 1-4 EEL = 889.9423 VDWAALS = -70.9988 EELEC = -1291.1795 EGB = -427.8488 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 16 TIME(PS) = 50.032 TEMP(K) = 322.59 PRESS = 0.0 Etot = -218.1980 EKtot = 242.3165 EPtot = -460.5146 BOND = 66.2284 ANGLE = 150.3313 DIHED = 160.3057 1-4 NB = 62.6238 1-4 EEL = 892.3681 VDWAALS = -71.4400 EELEC = -1294.3363 EGB = -426.5956 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 17 TIME(PS) = 50.034 TEMP(K) = 316.70 PRESS = 0.0 Etot = -217.6094 EKtot = 237.8920 EPtot = -455.5013 BOND = 67.6772 ANGLE = 153.4290 DIHED = 160.5302 1-4 NB = 62.5690 1-4 EEL = 894.5211 VDWAALS = -71.3802 EELEC = -1297.2513 EGB = -425.5962 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 18 TIME(PS) = 50.036 TEMP(K) = 315.08 PRESS = 0.0 Etot = -217.3240 EKtot = 236.6781 EPtot = -454.0020 BOND = 70.8008 ANGLE = 151.6109 DIHED = 160.2190 1-4 NB = 62.3195 1-4 EEL = 895.9743 VDWAALS = -70.7948 EELEC = -1298.9394 EGB = -425.1923 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 19 TIME(PS) = 50.038 TEMP(K) = 322.00 PRESS = 0.0 Etot = -217.8103 EKtot = 241.8710 EPtot = -459.6813 BOND = 69.3205 ANGLE = 146.8208 DIHED = 160.0041 1-4 NB = 61.9302 1-4 EEL = 896.5265 VDWAALS = -69.9068 EELEC = -1298.8994 EGB = -425.4771 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 20 TIME(PS) = 50.040 TEMP(K) = 328.52 PRESS = 0.0 Etot = -218.3814 EKtot = 246.7700 EPtot = -465.1514 BOND = 64.3848 ANGLE = 145.1483 DIHED = 160.2085 1-4 NB = 61.6679 1-4 EEL = 896.1871 VDWAALS = -69.1999 EELEC = -1297.2382 EGB = -426.3098 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) = 50.040 TEMP(K) = 322.77 PRESS = 0.0 Etot = -218.0751 EKtot = 242.4520 EPtot = -460.5271 BOND = 68.4967 ANGLE = 153.3168 DIHED = 158.4208 1-4 NB = 60.7577 1-4 EEL = 888.2649 VDWAALS = -70.5680 EELEC = -1291.1162 EGB = -428.0997 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 20 TIME(PS) = 50.040 TEMP(K) = 13.67 PRESS = 0.0 Etot = 0.6340 EKtot = 10.2664 EPtot = 10.7901 BOND = 5.3806 ANGLE = 6.5246 DIHED = 3.9410 1-4 NB = 2.4029 1-4 EEL = 4.1764 VDWAALS = 1.0729 EELEC = 5.0172 EGB = 2.5753 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 0.17 92.43 | Bond 0.00 0.00 | Angle 0.00 1.62 | Dihedral 0.01 4.32 | Shake 0.00 0.00 | RunMD 0.00 1.62 | Other 0.00 0.00 | ------------------------------ | Total 0.18 | Generalized Born CPU Time: | | Routine Sec % | ------------------------------------ | Radii Calc 0.04 21.08 | Diagonal Calc 0.07 38.38 | Off Diagonal Calc 0.06 32.97 | --------------------------------- | Total 0.17 92.43 | Setup CPU time: 0.01 seconds | NonSetup CPU time: 0.18 seconds | Total CPU time: 0.19 seconds 0.00 hours | Setup wall time: 0 seconds | NonSetup wall time: 1 seconds | Total wall time: 1 seconds 0.00 hours