------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 12/06/2011 at 15:59:35 [-O]verwriting output File Assignments: | MDIN: min.i | MDOUT: min_ex.log |INPCRD: 4ions2.inpcrd | PARM: 4ions_ex.prmtop |RESTRT: min_ex.rst | REFC: 4ions2.inpcrd | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj | Here is the input file: Minimization with Cartesian restraints &cntrl ntb=0, cut=12.0, imin=1, maxcyc=200, ntpr=5, ntr=1, restraint_wt=100.0, restraintmask=':1', / -------------------------------------------------------------------------------- 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 = 30.500 | New format PARM file being parsed. | Version = 1.000 Date = 12/06/11 Time = 15:38:03 NATOM = 4 NTYPES = 2 NBONH = 0 MBONA = 0 NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0 NHPARM = 0 NPARM = 0 NNB = 4 NRES = 4 NBONA = 0 NTHETA = 0 NPHIA = 0 NUMBND = 0 NUMANG = 0 NPTRA = 0 NATYP = 2 NPHB = 0 IFBOX = 0 NMXRS = 1 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 1396 | Hollerith 18 | Integer 20072 | Max Pairs 6 | nblistReal 48 | nblist Int 321361 | Total 1345 kbytes | Note: 1-4 EEL scale factors are being read from the topology file. | Note: 1-4 VDW scale factors are being read from the topology file. | 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 = 5, 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 Frozen or restrained atoms: ibelly = 0, ntr = 1 Energy minimization: maxcyc = 200, ncyc = 10, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES Mask :1; matches 1 atoms -------------------------------------------------------------------------------- 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 = 0.00000000 Forcing neutrality... -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- eedmeth=4: Setting switch to one everywhere --------------------------------------------------- | Local SIZE OF NONBOND LIST = 6 | TOTAL SIZE OF NONBOND LIST = 6 NSTEP ENERGY RMS GMAX NAME NUMBER 1 1.4856E+06 4.8150E+06 8.7660E+06 Cl- 4 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 1486183.1189 EEL = -566.8486 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 5 1.1043E+06 3.4661E+06 6.3240E+06 Cl- 4 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 1104890.5030 EEL = -549.9904 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0318 EAMBER = 1104340.5126 NSTEP ENERGY RMS GMAX NAME NUMBER 10 4.9629E+05 1.4136E+06 2.6033E+06 Cl- 4 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 496799.3858 EEL = -506.4696 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.4707 EAMBER = 496292.9162 NSTEP ENERGY RMS GMAX NAME NUMBER 15 4.1845E+04 8.5118E+04 1.4924E+05 Cl- 4 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 42225.1733 EEL = -387.0992 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 7.0702 EAMBER = 41838.0742 NSTEP ENERGY RMS GMAX NAME NUMBER 20 -1.8887E+02 3.6745E+01 7.5913E+01 Na+ 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 24.4499 EEL = -262.3753 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 49.0554 EAMBER = -237.9254 NSTEP ENERGY RMS GMAX NAME NUMBER 25 -2.8026E+02 2.5058E+01 5.6726E+01 Na+ 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 13.2999 EEL = -303.1833 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 9.6219 EAMBER = -289.8834 NSTEP ENERGY RMS GMAX NAME NUMBER 30 -2.8949E+02 1.8556E+01 4.0741E+01 Na+ 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 16.2716 EEL = -310.1565 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 4.3990 EAMBER = -293.8849 NSTEP ENERGY RMS GMAX NAME NUMBER 35 -3.0233E+02 1.6566E+01 3.3873E+01 Na+ 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 37.1477 EEL = -339.8943 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.4122 EAMBER = -302.7466 NSTEP ENERGY RMS GMAX NAME NUMBER 40 -3.0697E+02 3.1968E-01 6.9224E-01 Na+ 3 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 25.2035 EEL = -332.1762 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0017 EAMBER = -306.9726 NSTEP ENERGY RMS GMAX NAME NUMBER 45 -3.0698E+02 7.0947E-02 1.0462E-01 Cl- 4 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 24.8768 EEL = -331.8595 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0002 EAMBER = -306.9827 NSTEP ENERGY RMS GMAX NAME NUMBER 50 -3.0698E+02 7.1160E-02 1.3400E-01 Na+ 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 24.9160 EEL = -331.8995 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0003 EAMBER = -306.9835 NSTEP ENERGY RMS GMAX NAME NUMBER 55 1.3714E+03 2.2926E+02 6.9570E+02 Na+ 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.0828 EEL = -122.4944 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 1494.0020 EAMBER = -122.5772 NSTEP ENERGY RMS GMAX NAME NUMBER 60 -3.0698E+02 6.3624E-03 1.2767E-02 Na+ 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 24.8823 EEL = -331.8658 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 EAMBER = -306.9836 NSTEP ENERGY RMS GMAX NAME NUMBER 65 -3.0698E+02 1.7921E-05 2.6057E-05 Cl- 4 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 24.8747 EEL = -331.8583 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 EAMBER = -306.9836 FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 65 -3.0698E+02 1.7921E-05 2.6057E-05 Cl- 4 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = 24.8747 EEL = -331.8583 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 EAMBER = -306.9836 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.00 ( 1.83% of Total) | Fast Water setup 0.00 ( 0.06% of Total) | Build the list 0.01 (98.72% of List ) | Other 0.00 ( 1.28% of List ) | List time 0.01 (46.68% of Nonbo) | Short_ene time 0.01 (98.58% of Direc) | Other 0.00 ( 1.42% of Direc) | Direct Ewald time 0.01 (96.41% of Ewald) | Force Adjust 0.00 ( 0.52% of Ewald) | Virial junk 0.00 ( 0.58% of Ewald) | Start synchronizatio 0.00 ( 0.58% of Ewald) | Other 0.00 ( 1.90% of Ewald) | Ewald time 0.01 (52.22% of Nonbo) | IPS excludes 0.00 ( 0.15% of Nonbo) | Other 0.00 ( 0.96% of Nonbo) | Nonbond force 0.01 (97.55% of Force) | Bond/Angle/Dihedral 0.00 ( 0.61% of Force) | Other 0.00 ( 1.84% of Force) | Force time 0.01 (100.0% of Runmd) | Runmd Time 0.01 (52.33% of Total) | Other 0.01 (45.78% of Total) | Total time 0.02 (99.25% of ALL ) | Highest rstack allocated: 15 | Highest istack allocated: 3 | Job began at 15:59:35.284 on 12/06/2011 | Setup done at 15:59:35.289 on 12/06/2011 | Run done at 15:59:35.307 on 12/06/2011 | wallclock() was called 1529 times