------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 02/19/2004 at 13:55:03 [-O]verwriting output File Assignments: | MDIN: min.in | MDOUT: gcg_a.min.out |INPCRD: gcg_a.x | PARM: prmtop |RESTRT: gcg_a.min.x | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: energy minimization for DNA starting structures &cntrl imin=1, maxcyc=100, ncyc=50, ntpr=20, ntb=0, cut=10.0 / &ewald eedmeth=5, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation |Largest sphere to fit in unit cell has radius = 40.662 | New format PARM file being parsed. | Version = 1.000 Date = 02/18/04 Time = 18:03:14 NATOM = 632 NTYPES = 15 NBONH = 228 MBONA = 452 NTHETH = 536 MTHETA = 694 NPHIH = 946 MPHIA = 1122 NHPARM = 0 NPARM = 0 NNB = 3508 NRES = 20 NBONA = 452 NTHETA = 694 NPHIA = 1122 NUMBND = 37 NUMANG = 76 NPTRA = 34 NATYP = 25 NPHB = 0 IFBOX = 0 NMXRS = 33 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 50966 | Hollerith 3814 | Integer 962783 | Max Pairs 199396 | Max Rstack 56320 | Max Istack 3160 | Total 5405 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- 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 = 20, 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 = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 10.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 100, ncyc = 50, ntmin = 1 dx0 = 0.01000, dxm = 0.50000, drms = 0.00010 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 Sum of charges from parm topology file = -17.99999989 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- eedmeth=5: Using 1/r dielectric --------------------------------------------------- | Local SIZE OF NONBOND LIST = 43686 | TOTAL SIZE OF NONBOND LIST = 43686 NSTEP ENERGY RMS GMAX NAME NUMBER 1 2.5250E+02 3.1520E+01 3.9177E+02 H72 113 BOND = 51.6630 ANGLE = 112.0550 DIHED = 345.3028 VDWAALS = 601.1646 EEL = -197.1396 HBOND = 0.0000 1-4 VDW = 190.0440 1-4 EEL = -850.5871 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 20 -3.0990E+02 8.7624E+00 4.5296E+01 H72 113 BOND = 38.3296 ANGLE = 89.3436 DIHED = 341.6713 VDWAALS = 100.6563 EEL = -198.7053 HBOND = 0.0000 1-4 VDW = 180.6951 1-4 EEL = -861.8915 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 40 -6.5316E+02 6.6860E+00 8.9810E+01 C4 115 BOND = 38.9182 ANGLE = 100.7161 DIHED = 332.3410 VDWAALS = -206.1213 EEL = -177.2631 HBOND = 0.0000 1-4 VDW = 164.6569 1-4 EEL = -906.4039 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 60 -8.0513E+02 2.3958E+00 2.1328E+01 C6 108 BOND = 31.1321 ANGLE = 94.0471 DIHED = 323.8153 VDWAALS = -288.3583 EEL = -209.6185 HBOND = 0.0000 1-4 VDW = 150.2551 1-4 EEL = -906.4045 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 80 -8.5874E+02 9.2739E-01 5.5840E+00 H5'1 320 BOND = 22.4709 ANGLE = 85.2532 DIHED = 323.0779 VDWAALS = -311.0555 EEL = -232.2709 HBOND = 0.0000 1-4 VDW = 152.1840 1-4 EEL = -898.3970 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -8.8201E+02 1.2974E+00 7.1811E+00 O5' 318 BOND = 22.8670 ANGLE = 88.6053 DIHED = 315.3774 VDWAALS = -314.8159 EEL = -247.0330 HBOND = 0.0000 1-4 VDW = 151.8347 1-4 EEL = -898.8423 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 100 -8.8201E+02 1.2974E+00 7.1811E+00 O5' 318 BOND = 22.8670 ANGLE = 88.6053 DIHED = 315.3774 VDWAALS = -314.8159 EEL = -247.0330 HBOND = 0.0000 1-4 VDW = 151.8347 1-4 EEL = -898.8423 RESTRAINT = 0.0000 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.00 ( 0.37% of Total) | Build the list 0.11 (96.70% of List ) | Other 0.00 ( 3.30% of List ) | List time 0.12 (24.89% of Nonbo) | Short_ene time 0.34 (99.51% of Direc) | Other 0.00 ( 0.49% of Direc) | Direct Ewald time 0.34 (94.65% of Ewald) | Force Adjust 0.02 ( 4.47% of Ewald) | Virial junk 0.00 ( 0.68% of Ewald) | Start sycnronization 0.00 ( 0.10% of Ewald) | Other 0.00 ( 0.11% of Ewald) | Ewald time 0.36 (75.07% of Nonbo) | Other 0.00 ( 0.04% of Nonbo) | Nonbond force 0.48 (81.94% of Force) | Bond/Angle/Dihedral 0.10 (17.95% of Force) | Other 0.00 ( 0.12% of Force) | Force time 0.58 (100.0% of Runmd) | Runmd Time 0.58 (83.23% of Total) | Other 0.11 (16.39% of Total) | Total time 0.70 (100.0% of ALL ) | Highest rstack allocated: 20632 | Highest istack allocated: 168 | Job began at 13:55:03.301 on 02/19/2004 | Setup done at 13:55:03.342 on 02/19/2004 | Run done at 13:55:04.000 on 02/19/2004 | wallclock() was called 1818 times