------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 08/13/2004 at 16:40:12 [-O]verwriting output File Assignments: | MDIN: min_classical.in | MDOUT: min_classical.out |INPCRD: NMA.inpcrd | PARM: NMA.prmtop |RESTRT: NMA_min_classical.crd | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Initial minimisation of our structure &cntrl imin=1, maxcyc=500, ncyc=200, cut=20, ntb=0, fcap=1.5, /   -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation |Largest sphere to fit in unit cell has radius = 44.093 | New format PARM file being parsed. | Version = 1.000 Date = 08/13/04 Time = 16:17:36 NATOM = 1239 NTYPES = 9 NBONH = 1234 MBONA = 4 NTHETH = 14 MTHETA = 4 NPHIH = 21 MPHIA = 3 NHPARM = 0 NPARM = 0 NNB = 1682 NRES = 411 NBONA = 4 NTHETA = 4 NPHIA = 3 NUMBND = 9 NUMANG = 10 NPTRA = 7 NATYP = 9 NPHB = 1 IFBOX = 0 NMXRS = 6 IFCAP = 1 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 97652 | Hollerith 7847 | Integer 192517 | Max Pairs 766941 | Max Rstack 62390 | Max Istack 6195 | Total 5053 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 = 20.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 500, ncyc = 200, ntmin = 1 dx0 = 0.01000, drms = 0.00010 Water cap: ivcap = 0, natcap = 12 fcap = 1.50000, cutcap = 15.00000 xcap = 2.71135, ycap = 1.22332, zcap = -1.12736 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 409 Sum of charges from parm topology file = 0.00000000 Forcing neutrality... -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- eedmeth=4: Setting switch to one everywhere --------------------------------------------------- | Local SIZE OF NONBOND LIST = 601315 | TOTAL SIZE OF NONBOND LIST = 601315 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -2.8665E+03 1.1491E+01 4.3881E+01 O 1144 BOND = 0.0199 ANGLE = 0.0041 DIHED = 2.4829 VDWAALS = 404.4459 EEL = -3256.1309 HBOND = 0.0000 1-4 VDW = 1.3655 1-4 EEL = -18.6622 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 50 -3.1678E+03 1.4182E+00 6.1274E+00 H1 230 BOND = 204.1173 ANGLE = 0.2887 DIHED = 2.5065 VDWAALS = 436.4259 EEL = -3792.3472 HBOND = 0.0000 1-4 VDW = 0.9633 1-4 EEL = -19.7282 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -3.0929E+03 3.1819E+00 1.6104E+01 H1 437 BOND = 204.6507 ANGLE = 0.3633 DIHED = 2.5050 VDWAALS = 488.9918 EEL = -3770.4491 HBOND = 0.0000 1-4 VDW = 0.9136 1-4 EEL = -19.8759 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 150 -2.9510E+03 1.0419E+00 4.4002E+00 H1 437 BOND = 248.5015 ANGLE = 0.3967 DIHED = 2.5059 VDWAALS = 534.4890 EEL = -3717.8784 HBOND = 0.0000 1-4 VDW = 0.8990 1-4 EEL = -19.9209 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -2.8295E+03 2.4719E+00 1.4525E+01 H1 437 BOND = 278.0956 ANGLE = 0.4114 DIHED = 2.5083 VDWAALS = 571.8798 EEL = -3663.3911 HBOND = 0.0000 1-4 VDW = 0.8930 1-4 EEL = -19.9324 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 250 -3.0979E+03 3.1952E+00 3.5057E+01 O 361 BOND = 311.5286 ANGLE = 0.7672 DIHED = 2.5416 VDWAALS = 765.6555 EEL = -4159.1559 HBOND = 0.0000 1-4 VDW = 1.0009 1-4 EEL = -20.2183 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 300 -2.9307E+03 2.2396E+00 4.0140E+01 C 5 BOND = 318.4570 ANGLE = 0.5934 DIHED = 2.5365 VDWAALS = 826.2689 EEL = -4059.5283 HBOND = 0.0000 1-4 VDW = 0.9668 1-4 EEL = -20.0233 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 350 -3.1700E+03 2.3805E+00 4.6760E+01 N 7 BOND = 318.8449 ANGLE = 0.8324 DIHED = 2.5300 VDWAALS = 854.1851 EEL = -4327.2929 HBOND = 0.0000 1-4 VDW = 0.9602 1-4 EEL = -20.0481 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 400 -3.0718E+03 1.4371E+00 3.2928E+01 C 5 BOND = 322.0390 ANGLE = 0.9423 DIHED = 2.5147 VDWAALS = 882.3583 EEL = -4260.4683 HBOND = 0.0000 1-4 VDW = 0.9750 1-4 EEL = -20.1926 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 450 -2.5988E+03 1.5159E+00 2.7259E+01 O 6 BOND = 342.0691 ANGLE = 0.4973 DIHED = 2.5074 VDWAALS = 914.5257 EEL = -3839.8154 HBOND = 0.0000 1-4 VDW = 0.7589 1-4 EEL = -19.3499 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 500 -2.8333E+03 1.1659E+00 2.4210E+01 C 5 BOND = 344.6722 ANGLE = 0.6147 DIHED = 2.4711 VDWAALS = 935.3651 EEL = -4097.3700 HBOND = 0.0000 1-4 VDW = 0.8346 1-4 EEL = -19.9098 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 500 -2.8333E+03 1.1659E+00 2.4210E+01 C 5 BOND = 344.6722 ANGLE = 0.6147 DIHED = 2.4711 VDWAALS = 935.3651 EEL = -4097.3700 HBOND = 0.0000 1-4 VDW = 0.8346 1-4 EEL = -19.9098 RESTRAINT = 0.0000 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.01 ( 0.02% of Total) | Build the list 0.64 (99.14% of List ) | Other 0.01 ( 0.86% of List ) | List time 0.65 ( 2.93% of Nonbo) | Short_ene time 21.38 (99.89% of Direc) | Other 0.02 ( 0.11% of Direc) | Direct Ewald time 21.40 (99.84% of Ewald) | Force Adjust 0.01 ( 0.04% of Ewald) | Virial junk 0.02 ( 0.09% of Ewald) | Start sycnronization 0.00 ( 0.02% of Ewald) | Other 0.00 ( 0.01% of Ewald) | Ewald time 21.43 (97.06% of Nonbo) | Nonbond force 22.08 (99.70% of Force) | Bond/Angle/Dihedral 0.05 ( 0.21% of Force) | Other 0.02 ( 0.09% of Force) | Force time 22.15 (100.0% of Runmd) | Runmd Time 22.15 (99.11% of Total) | Other 0.19 ( 0.87% of Total) | Total time 22.35 (100.0% of ALL ) | Highest rstack allocated: 19723 | Highest istack allocated: 1089 | Job began at 16:40:12.718 on 08/13/2004 | Setup done at 16:40:12.804 on 08/13/2004 | Run done at 16:40:35.066 on 08/13/2004 | wallclock() was called 9050 times