------------------------------------------------------- Amber 9 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 06/02/2005 at 14:29:48 [-O]verwriting output File Assignments: | MDIN: min1.in | MDOUT: min1.out |INPCRD: TC5b.inpcrd | PARM: TC5b.prmtop |RESTRT: min1.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Stage 1 - minimisation of TC5b &cntrl imin=1, maxcyc=1000, ncyc=500, cut=999., rgbmax=999.,igb=1, ntb=0, ntpr=100, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: SGIFFT MPI | New format PARM file being parsed. | Version = 1.000 Date = 06/02/05 Time = 14:13:53 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 | Memory Use Allocated | Real 12349 | Hollerith 1846 | Integer 35106 | Max Pairs 1 | Max Rstack 1 | Max Istack 1 | nblistReal 0 | nblist Int 0 | Total 240 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- NASN General flags: imin = 1, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 100, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 1, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 999.00000, 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 = 999.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 1000, ncyc = 500, ntmin = 1 dx0 = 0.01000, drms = 0.00010 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- NASN begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 | Atom division among processors: | 0 35 56 75 92 116 116 135 | 157 176 197 219 250 250 278 292 | 304 | Running AMBER/MPI version on 16 nodes -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NSTEP ENERGY RMS GMAX NAME NUMBER 1 3.8227E+06 3.6500E+06 5.9207E+07 HD2 253 BOND = 13.6690 ANGLE = 38.7157 DIHED = 113.6281 VDWAALS = 3823253.7155 EEL = -1313.2880 EGB = -396.0814 1-4 VDW = 103.7261 1-4 EEL = 911.7746 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -5.8939E+02 1.1154E+00 5.4833E+00 HG2 256 BOND = 14.1175 ANGLE = 51.8488 DIHED = 123.5659 VDWAALS = -20.3988 EEL = -1296.7794 EGB = -415.5712 1-4 VDW = 63.8807 1-4 EEL = 889.9459 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -6.2910E+02 1.8443E+00 1.4110E+01 C 115 BOND = 15.4601 ANGLE = 47.2070 DIHED = 116.3527 VDWAALS = -39.4208 EEL = -1286.7241 EGB = -420.7227 1-4 VDW = 57.6996 1-4 EEL = 881.0514 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 300 -6.4403E+02 1.5711E+00 1.2462E+01 CG 100 BOND = 15.5370 ANGLE = 45.6882 DIHED = 112.1846 VDWAALS = -44.7967 EEL = -1278.8223 EGB = -424.1089 1-4 VDW = 55.0091 1-4 EEL = 875.2820 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 400 -6.5282E+02 3.4292E-01 1.6192E+00 CG 100 BOND = 15.3097 ANGLE = 44.7824 DIHED = 109.3727 VDWAALS = -47.1697 EEL = -1273.1291 EGB = -426.5229 1-4 VDW = 53.3534 1-4 EEL = 871.1849 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 500 -6.5864E+02 2.9018E-01 1.4056E+00 CD2 114 BOND = 15.3040 ANGLE = 44.1002 DIHED = 107.1774 VDWAALS = -48.5489 EEL = -1268.9458 EGB = -428.3935 1-4 VDW = 52.2543 1-4 EEL = 868.4157 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 600 -6.7924E+02 6.6192E-01 4.7520E+00 N 293 BOND = 14.5255 ANGLE = 40.7027 DIHED = 98.9937 VDWAALS = -52.7097 EEL = -1258.2089 EGB = -434.8000 1-4 VDW = 49.8248 1-4 EEL = 862.4271 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 700 -6.8786E+02 8.0013E-01 5.0332E+00 C 263 BOND = 13.8601 ANGLE = 37.5805 DIHED = 96.4698 VDWAALS = -54.4601 EEL = -1260.9695 EGB = -434.8440 1-4 VDW = 50.0876 1-4 EEL = 864.4171 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 800 -6.9293E+02 6.6361E-01 4.1402E+00 C 263 BOND = 13.6110 ANGLE = 36.4172 DIHED = 95.5184 VDWAALS = -55.5117 EEL = -1258.4744 EGB = -435.9911 1-4 VDW = 49.1448 1-4 EEL = 862.3537 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 900 -6.9743E+02 6.2613E-01 2.9779E+00 CZ3 110 BOND = 13.0014 ANGLE = 35.7245 DIHED = 94.7248 VDWAALS = -57.0979 EEL = -1261.2878 EGB = -434.4786 1-4 VDW = 48.9247 1-4 EEL = 863.0598 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1000 -6.9897E+02 1.9473E-01 9.6362E-01 CD1 44 BOND = 12.9092 ANGLE = 35.0330 DIHED = 94.7732 VDWAALS = -57.3368 EEL = -1261.7824 EGB = -433.5778 1-4 VDW = 48.6629 1-4 EEL = 862.3478 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1000 -6.9897E+02 1.9473E-01 9.6362E-01 CD1 44 BOND = 12.9092 ANGLE = 35.0330 DIHED = 94.7732 VDWAALS = -57.3368 EEL = -1261.7824 EGB = -433.5778 1-4 VDW = 48.6629 1-4 EEL = 862.3478 RESTRAINT = 0.0000 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.00 ( 0.02% of Total) | Calc gb radii 0.59 (22.38% of Gen B) | Communicate gb radii 0.38 (14.44% of Gen B) | Calc gb diag 0.80 (30.24% of Gen B) | Calc gb off-diag 0.82 (30.85% of Gen B) | Other 0.06 ( 2.10% of Gen B) | Gen Born time 2.65 (98.62% of Nonbo) | IPS excludes 0.04 ( 1.38% of Nonbo) | Nonbond force 2.69 (80.86% of Force) | Bond/Angle/Dihedral 0.07 ( 1.96% of Force) | FRC Collect time 0.16 ( 4.78% of Force) | Other 0.41 (12.40% of Force) | Force time 3.33 (100.0% of Runmd) | Runmd Time 3.33 (90.27% of Total) | Other 0.36 ( 9.71% of Total) | Total time 3.68 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 14:29:48.488 on 06/02/2005 | Setup done at 14:29:48.543 on 06/02/2005 | Run done at 14:29:52.173 on 06/02/2005 | wallclock() was called 22008 times