------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 04/06/2007 at 15:36:38 [-O]verwriting output File Assignments: | MDIN: analyze.in | MDOUT: analyze.out |INPCRD: Xe2.prmcrd | PARM: Xe2.prmtop |RESTRT: Xe2.restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: Xe2.x |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: &cntrl imin = 5, ntx = 1, irest = 0, ntrx = 1, ntxo = 1, ntpr = 1, ntwx = 1000, ntwe = 1000, cut = 9999.0, igb = 6, ntb=0, ntt=3,gamma_ln=5.0, maxcyc = 1, t = 0.0, dt = 0.001, temp0 = 300.0, tempi = 300.0, &end -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 04/05/07 Time = 15:49:59 NATOM = 2 NTYPES = 1 NBONH = 0 MBONA = 0 NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0 NHPARM = 0 NPARM = 0 NNB = 2 NRES = 2 NBONA = 0 NTHETA = 0 NPHIA = 0 NUMBND = 0 NUMANG = 0 NPTRA = 0 NATYP = 1 NPHB = 0 IFBOX = 0 NMXRS = 1 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 255 | Hollerith 16 | Integer 20031 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 80 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 5, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 1000, ntwv = 0, ntwe = 1000 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 6, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut =9999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500 rdt = 0.00000, rgbmax = 25.00000 alpb = 0 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 1, ncyc = 10, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- POST-PROCESSING OF TRAJECTORY ENERGIES minimizing coord set # 1 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -2.9241E-01 1.1137E-01 1.1517E-01 Xe 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.2924 EEL = 0.0000 EGB = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -2.9241E-01 1.1137E-01 1.1517E-01 Xe 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.2924 EEL = 0.0000 EGB = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 minimization completed, ENE= -.292405E+00 RMS= 0.111366E+00 minimizing coord set # 2 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -2.6500E-01 1.0263E-01 1.5465E-01 Xe 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.2650 EEL = 0.0000 EGB = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -2.6500E-01 1.0263E-01 1.5465E-01 Xe 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.2650 EEL = 0.0000 EGB = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 minimization completed, ENE= -.265002E+00 RMS= 0.102630E+00 minimizing coord set # 3 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.4358E-01 5.5671E-02 9.4512E-02 Xe 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.1436 EEL = 0.0000 EGB = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.4358E-01 5.5671E-02 9.4512E-02 Xe 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.1436 EEL = 0.0000 EGB = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 minimization completed, ENE= -.143585E+00 RMS= 0.556706E-01 minimizing coord set # 4 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -2.0323E-01 7.9910E-02 1.3141E-01 Xe 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.2032 EEL = 0.0000 EGB = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -2.0323E-01 7.9910E-02 1.3141E-01 Xe 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.2032 EEL = 0.0000 EGB = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 minimization completed, ENE= -.203231E+00 RMS= 0.799099E-01 minimizing coord set # 5 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0890E-01 4.1191E-02 7.1273E-02 Xe 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.1089 EEL = 0.0000 EGB = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0890E-01 4.1191E-02 7.1273E-02 Xe 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.1089 EEL = 0.0000 EGB = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 minimization completed, ENE= -.108904E+00 RMS= 0.411915E-01 minimizing coord set # 6 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.0168E-02 1.3333E-02 2.1016E-02 Xe 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.0402 EEL = 0.0000 EGB = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.0168E-02 1.3333E-02 2.1016E-02 Xe 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.0402 EEL = 0.0000 EGB = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 minimization completed, ENE= -.401679E-01 RMS= 0.133335E-01 minimizing coord set # 7 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -6.2646E-02 2.2152E-02 2.8276E-02 Xe 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.0626 EEL = 0.0000 EGB = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -6.2646E-02 2.2152E-02 2.8276E-02 Xe 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.0626 EEL = 0.0000 EGB = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 minimization completed, ENE= -.626460E-01 RMS= 0.221523E-01 minimizing coord set # 8 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.9884E-01 2.6255E-02 3.9179E-02 Xe 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.4988 EEL = 0.0000 EGB = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.9884E-01 2.6255E-02 3.9179E-02 Xe 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.4988 EEL = 0.0000 EGB = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 minimization completed, ENE= -.498840E+00 RMS= 0.262551E-01 minimizing coord set # 9 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -2.8070E-01 1.0776E-01 1.8561E-01 Xe 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.2807 EEL = 0.0000 EGB = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -2.8070E-01 1.0776E-01 1.8561E-01 Xe 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.2807 EEL = 0.0000 EGB = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 minimization completed, ENE= -.280696E+00 RMS= 0.107763E+00 minimizing coord set # 10 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.6839E-01 1.8860E-01 2.7716E-01 Xe 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.4684 EEL = 0.0000 EGB = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 1 -4.6839E-01 1.8860E-01 2.7716E-01 Xe 1 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -0.4684 EEL = 0.0000 EGB = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 minimization completed, ENE= -.468386E+00 RMS= 0.188600E+00 Trajectory file ended -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.00 (12.74% of Total) | Fast Water setup 0.00 ( 0.06% of Total) | Nonbond force 0.00 (39.57% of Force) | Bond/Angle/Dihedral 0.00 (15.15% of Force) | Other 0.00 (45.28% of Force) | Force time 0.00 (100.0% of Runmd) | Runmd Time 0.00 ( 0.77% of Total) | Other 0.01 (86.42% of Total) | Total time 0.02 (99.51% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 | Job began at 15:36:38.748 on 04/06/2007 | Setup done at 15:36:38.762 on 04/06/2007 | Run done at 15:36:38.763 on 04/06/2007 | wallclock() was called 128 times