------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 02/19/2004 at 13:55:07 [-O]verwriting output File Assignments: | MDIN: min.in | MDOUT: gcg_b.min.out |INPCRD: gcg_b.x | PARM: prmtop |RESTRT: gcg_b.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 = 39.759 | 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 51007 | Hollerith 3814 | Integer 956383 | Max Pairs 199396 | Max Rstack 56320 | Max Istack 3160 | Total 5380 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 = 48174 | TOTAL SIZE OF NONBOND LIST = 48174 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -2.3461E+02 2.6294E+01 1.6810E+02 H2'2 157 BOND = 60.2565 ANGLE = 96.8244 DIHED = 340.8917 VDWAALS = 413.3599 EEL = -534.5588 HBOND = 0.0000 1-4 VDW = 233.0032 1-4 EEL = -844.3908 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 20 -9.1420E+02 2.3982E+00 1.0671E+01 O2P 129 BOND = 23.3342 ANGLE = 126.0144 DIHED = 332.8663 VDWAALS = -168.6732 EEL = -526.2005 HBOND = 0.0000 1-4 VDW = 179.6366 1-4 EEL = -881.1817 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 40 -1.0013E+03 1.2232E+00 5.5293E+00 H71 112 BOND = 24.7930 ANGLE = 117.2947 DIHED = 329.3272 VDWAALS = -226.1772 EEL = -520.2410 HBOND = 0.0000 1-4 VDW = 165.7817 1-4 EEL = -892.0845 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 60 -1.0618E+03 1.3940E+00 1.5543E+01 O5' 2 BOND = 25.4925 ANGLE = 115.3131 DIHED = 326.1568 VDWAALS = -277.9600 EEL = -521.5312 HBOND = 0.0000 1-4 VDW = 158.6703 1-4 EEL = -887.9611 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 80 -1.0727E+03 1.1709E+00 5.0312E+00 H71 112 BOND = 21.5210 ANGLE = 116.1253 DIHED = 317.9787 VDWAALS = -303.4550 EEL = -490.1717 HBOND = 0.0000 1-4 VDW = 156.4304 1-4 EEL = -891.1208 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -1.0863E+03 1.8409E+00 1.1724E+01 C4 184 BOND = 23.3213 ANGLE = 101.4567 DIHED = 309.7184 VDWAALS = -301.2000 EEL = -484.9180 HBOND = 0.0000 1-4 VDW = 158.4468 1-4 EEL = -893.0894 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 100 -1.0863E+03 1.8409E+00 1.1724E+01 C4 184 BOND = 23.3213 ANGLE = 101.4567 DIHED = 309.7184 VDWAALS = -301.2000 EEL = -484.9180 HBOND = 0.0000 1-4 VDW = 158.4468 1-4 EEL = -893.0894 RESTRAINT = 0.0000 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.00 ( 0.37% of Total) | Build the list 0.11 (96.64% of List ) | Other 0.00 ( 3.36% of List ) | List time 0.11 (22.40% of Nonbo) | Short_ene time 0.37 (99.57% of Direc) | Other 0.00 ( 0.43% of Direc) | Direct Ewald time 0.38 (95.09% of Ewald) | Force Adjust 0.02 ( 4.11% of Ewald) | Virial junk 0.00 ( 0.61% of Ewald) | Start sycnronization 0.00 ( 0.09% of Ewald) | Other 0.00 ( 0.10% of Ewald) | Ewald time 0.40 (77.57% of Nonbo) | Other 0.00 ( 0.03% of Nonbo) | Nonbond force 0.51 (82.88% of Force) | Bond/Angle/Dihedral 0.10 (17.03% of Force) | Other 0.00 ( 0.09% of Force) | Force time 0.62 (100.0% of Runmd) | Runmd Time 0.62 (84.78% of Total) | Other 0.11 (14.85% of Total) | Total time 0.73 (100.0% of ALL ) | Highest rstack allocated: 20632 | Highest istack allocated: 170 | Job began at 13:55:07.770 on 02/19/2004 | Setup done at 13:55:07.809 on 02/19/2004 | Run done at 13:55:08.496 on 02/19/2004 | wallclock() was called 1818 times