------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 07/10/2007 at 14:55:02 [-O]verwriting output File Assignments: | MDIN: vac_min.in | MDOUT: vac_min.out |INPCRD: eqmecycl.inpcrd | PARM: eqmecycl.prmtop |RESTRT: vac_min.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: # eqaeqb: initial minimisation prior to MD &cntrl imin = 1, maxcyc = 500, ncyc = 250, ntb = 0, igb = 0, cut = 12 / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation | *** cutoff > system size, list only builds once |Largest sphere to fit in unit cell has radius = 31.646 | New format PARM file being parsed. | Version = 1.000 Date = 07/10/07 Time = 22:40:17 NATOM = 21 NTYPES = 2 NBONH = 14 MBONA = 7 NTHETH = 34 MTHETA = 8 NPHIH = 55 MPHIA = 24 NHPARM = 0 NPARM = 0 NNB = 124 NRES = 1 NBONA = 7 NTHETA = 8 NPHIA = 24 NUMBND = 2 NUMANG = 3 NPTRA = 5 NATYP = 2 NPHB = 0 IFBOX = 0 NMXRS = 21 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 2506 | Hollerith 129 | Integer 22064 | Max Pairs 210 | nblistReal 252 | nblist Int 366345 | Total 1540 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- UNK 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 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- UNK begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 Sum of charges from parm topology file = 0.00001000 Forcing neutrality... -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- eedmeth=4: Setting switch to one everywhere --------------------------------------------------- | Local SIZE OF NONBOND LIST = 87 | TOTAL SIZE OF NONBOND LIST = 87 NSTEP ENERGY RMS GMAX NAME NUMBER 1 8.2251E+00 9.2830E+00 2.0759E+01 C2 10 BOND = 1.4473 ANGLE = 0.8114 DIHED = 3.6158 VDWAALS = -0.7688 EEL = 1.8323 HBOND = 0.0000 1-4 VDW = 3.5719 1-4 EEL = -2.2848 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 50 6.0949E+00 1.1155E-01 4.4749E-01 C3 13 BOND = 0.2022 ANGLE = 0.3216 DIHED = 3.5576 VDWAALS = -0.8154 EEL = 1.8375 HBOND = 0.0000 1-4 VDW = 3.2386 1-4 EEL = -2.2473 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 100 6.0932E+00 2.7452E-02 7.6437E-02 C1 7 BOND = 0.2097 ANGLE = 0.3338 DIHED = 3.5612 VDWAALS = -0.8186 EEL = 1.8357 HBOND = 0.0000 1-4 VDW = 3.2152 1-4 EEL = -2.2439 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 150 6.0929E+00 1.6798E-02 5.0804E-02 C1 7 BOND = 0.2111 ANGLE = 0.3351 DIHED = 3.5623 VDWAALS = -0.8191 EEL = 1.8355 HBOND = 0.0000 1-4 VDW = 3.2113 1-4 EEL = -2.2433 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 200 6.0928E+00 4.6508E-03 1.4051E-02 H5 14 BOND = 0.2105 ANGLE = 0.3356 DIHED = 3.5627 VDWAALS = -0.8192 EEL = 1.8353 HBOND = 0.0000 1-4 VDW = 3.2108 1-4 EEL = -2.2431 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 250 6.0927E+00 3.3847E-03 9.8929E-03 H5 14 BOND = 0.2106 ANGLE = 0.3358 DIHED = 3.5628 VDWAALS = -0.8192 EEL = 1.8353 HBOND = 0.0000 1-4 VDW = 3.2105 1-4 EEL = -2.2431 RESTRAINT = 0.0000 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 274 6.0927E+00 7.6096E-05 1.9228E-04 H6 15 BOND = 0.2104 ANGLE = 0.3358 DIHED = 3.5630 VDWAALS = -0.8192 EEL = 1.8353 HBOND = 0.0000 1-4 VDW = 3.2104 1-4 EEL = -2.2430 RESTRAINT = 0.0000 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.00 ( 0.92% of Total) | Fast Water setup 0.00 ( 0.03% of Total) | Build the list 0.00 (93.03% of List ) | Other 0.00 ( 6.97% of List ) | List time 0.00 (25.75% of Nonbo) | Short_ene time 0.00 (93.57% of Direc) | Other 0.00 ( 6.43% of Direc) | Direct Ewald time 0.01 (70.13% of Ewald) | Force Adjust 0.00 (21.55% of Ewald) | Virial junk 0.00 ( 1.49% of Ewald) | Start sycnronization 0.00 ( 1.57% of Ewald) | Other 0.00 ( 5.26% of Ewald) | Ewald time 0.01 (68.96% of Nonbo) | IPS excludes 0.00 ( 0.79% of Nonbo) | Other 0.00 ( 4.50% of Nonbo) | Nonbond force 0.01 (51.73% of Force) | Bond/Angle/Dihedral 0.01 (45.95% of Force) | Other 0.00 ( 2.33% of Force) | Force time 0.02 (100.0% of Runmd) | Runmd Time 0.02 (64.64% of Total) | Other 0.01 (34.42% of Total) | Total time 0.03 (99.76% of ALL ) | Highest rstack allocated: 50 | Highest istack allocated: 10 | Job began at 14:55:02.872 on 07/10/2007 | Setup done at 14:55:02.882 on 07/10/2007 | Run done at 14:55:02.904 on 07/10/2007 | wallclock() was called 6312 times