------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 02/20/2004 at 11:13:43 [-O]verwriting output File Assignments: | MDIN: polyAT_vac_init_min.in | MDOUT: polyAT_vac_init_min.out |INPCRD: polyAT_vac.inpcrd | PARM: polyAT_vac.prmtop |RESTRT: polyAT_vac_init_min.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: polyA-polyT 10-mer: initial minimisation prior to MD &cntrl imin = 1, maxcyc = 500, ncyc = 250, ntb = 0, igb = 0, cut = 12 &end -------------------------------------------------------------------------------- 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 = 02/19/04 Time = 15:33:29 NATOM = 638 NTYPES = 14 NBONH = 234 MBONA = 452 NTHETH = 554 MTHETA = 694 NPHIH = 1056 MPHIA = 1238 NHPARM = 0 NPARM = 0 NNB = 3544 NRES = 20 NBONA = 452 NTHETA = 694 NPHIA = 1238 NUMBND = 32 NUMANG = 59 NPTRA = 39 NATYP = 24 NPHB = 0 IFBOX = 0 NMXRS = 33 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 51442 | Hollerith 3850 | Integer 591341 | Max Pairs 203203 | Max Rstack 56380 | Max Istack 3190 | Total 3973 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 = 50, 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 = 12.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 500, ncyc = 250, ntmin = 1 dx0 = 0.01000, 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 = -17.99999992 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- eedmeth=4: Setting switch to one everywhere --------------------------------------------------- | Local SIZE OF NONBOND LIST = 73167 | TOTAL SIZE OF NONBOND LIST = 73167 NSTEP ENERGY RMS GMAX NAME NUMBER 1 9.2064E+01 4.9542E+01 6.8763E+02 O5' 321 BOND = 929.3608 ANGLE = 544.5351 DIHED = 467.8807 VDWAALS = 150.6633 EEL = -1984.8745 HBOND = 0.0000 1-4 VDW = 264.8124 1-4 EEL = -280.3135 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 50 -2.1645E+03 1.7242E+00 1.0015E+01 O5' 321 BOND = 22.9796 ANGLE = 124.3944 DIHED = 434.4160 VDWAALS = -225.5524 EEL = -2338.1529 HBOND = 0.0000 1-4 VDW = 176.9807 1-4 EEL = -359.6077 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -1.8337E+03 9.5341E-01 5.6203E+00 P 510 BOND = 20.5641 ANGLE = 111.9758 DIHED = 422.4239 VDWAALS = -264.9790 EEL = -1943.4585 HBOND = 0.0000 1-4 VDW = 173.2762 1-4 EEL = -353.5356 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 150 -1.9349E+03 6.9268E-01 4.0578E+00 P 478 BOND = 19.5023 ANGLE = 110.7216 DIHED = 417.5744 VDWAALS = -288.6293 EEL = -2012.7385 HBOND = 0.0000 1-4 VDW = 170.4104 1-4 EEL = -351.6989 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -2.0906E+03 1.3714E+00 1.5703E+01 P 478 BOND = 18.7939 ANGLE = 108.5088 DIHED = 413.6139 VDWAALS = -302.7286 EEL = -2146.5180 HBOND = 0.0000 1-4 VDW = 168.5579 1-4 EEL = -350.8134 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 250 -2.2813E+03 4.3369E-01 2.0546E+00 H72 624 BOND = 17.2589 ANGLE = 106.9147 DIHED = 410.1460 VDWAALS = -312.5599 EEL = -2320.3415 HBOND = 0.0000 1-4 VDW = 167.2711 1-4 EEL = -349.9438 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 300 -2.2945E+03 7.9440E-01 4.7007E+00 N1 362 BOND = 16.4212 ANGLE = 101.1746 DIHED = 397.9377 VDWAALS = -344.7720 EEL = -2279.8666 HBOND = 0.0000 1-4 VDW = 163.4382 1-4 EEL = -348.8008 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 350 -2.3678E+03 6.0376E-01 4.3894E+00 P 382 BOND = 16.1151 ANGLE = 97.5513 DIHED = 396.3728 VDWAALS = -344.9198 EEL = -2349.4362 HBOND = 0.0000 1-4 VDW = 163.5794 1-4 EEL = -347.0788 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 400 -2.3455E+03 5.5734E-01 4.5676E+00 P 382 BOND = 16.2303 ANGLE = 96.2071 DIHED = 395.2235 VDWAALS = -345.6651 EEL = -2323.3151 HBOND = 0.0000 1-4 VDW = 162.8481 1-4 EEL = -347.0110 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 450 -2.3536E+03 6.0316E-01 4.0517E+00 P 382 BOND = 16.1789 ANGLE = 94.9383 DIHED = 394.0325 VDWAALS = -346.0808 EEL = -2329.2366 HBOND = 0.0000 1-4 VDW = 162.5522 1-4 EEL = -346.0154 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 500 -2.2929E+03 5.7810E-01 3.4109E+00 N1 362 BOND = 16.0918 ANGLE = 93.9850 DIHED = 392.9956 VDWAALS = -346.6892 EEL = -2266.4257 HBOND = 0.0000 1-4 VDW = 162.1781 1-4 EEL = -345.0298 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 500 -2.2929E+03 5.7810E-01 3.4109E+00 N1 362 BOND = 16.0918 ANGLE = 93.9850 DIHED = 392.9956 VDWAALS = -346.6892 EEL = -2266.4257 HBOND = 0.0000 1-4 VDW = 162.1781 1-4 EEL = -345.0298 RESTRAINT = 0.0000 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.02 ( 0.41% of Total) | Build the list 0.25 (88.34% of List ) | Other 0.03 (11.66% of List ) | List time 0.28 ( 7.92% of Nonbo) | Short_ene time 3.14 (99.64% of Direc) | Other 0.01 ( 0.36% of Direc) | Direct Ewald time 3.16 (97.11% of Ewald) | Force Adjust 0.08 ( 2.43% of Ewald) | Virial junk 0.01 ( 0.33% of Ewald) | Start sycnronization 0.00 ( 0.07% of Ewald) | Other 0.00 ( 0.06% of Ewald) | Ewald time 3.25 (92.06% of Nonbo) | Other 0.00 ( 0.02% of Nonbo) | Nonbond force 3.53 (83.10% of Force) | Bond/Angle/Dihedral 0.71 (16.83% of Force) | Other 0.00 ( 0.07% of Force) | Force time 4.25 (100.0% of Runmd) | Runmd Time 4.25 (97.41% of Total) | Other 0.10 ( 2.18% of Total) | Total time 4.36 (100.0% of ALL ) | Highest rstack allocated: 20397 | Highest istack allocated: 259 | Job began at 11:13:43.503 on 02/20/2004 | Setup done at 11:13:43.556 on 02/20/2004 | Run done at 11:13:47.864 on 02/20/2004 | wallclock() was called 9050 times