------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 04/22/2006 at 14:36:40 [-O]verwriting output File Assignments: | MDIN: min_classical.in | MDOUT: min_classical.out |INPCRD: NMA.inpcrd | PARM: NMA.prmtop |RESTRT: min_classical.rst | 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=8.0, ntb=1, ntc=2, ntf=2 / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read | peek_ewald_inpcrd: Box info found |Largest sphere to fit in unit cell has radius = 19.430 | New format PARM file being parsed. | Version = 1.000 Date = 04/22/06 Time = 14:22:14 NATOM = 4578 NTYPES = 9 NBONH = 4573 MBONA = 4 NTHETH = 14 MTHETA = 4 NPHIH = 22 MPHIA = 3 NHPARM = 0 NPARM = 0 NNB = 6134 NRES = 1524 NBONA = 4 NTHETA = 4 NPHIA = 3 NUMBND = 9 NUMANG = 10 NPTRA = 7 NATYP = 9 NPHB = 1 IFBOX = 1 NMXRS = 6 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 359215 | Hollerith 28994 | Integer 119793 | Max Pairs 1526000 | nblistReal 54936 | nblist Int 248585 | Total 10748 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 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 = 2, ntb = 1, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 8.00000, 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 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 0 Box X = 38.861 Box Y = 40.343 Box Z = 40.136 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 40 NFFT2 = 40 NFFT3 = 40 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 1522 Sum of charges from parm topology file = 0.00000000 Forcing neutrality... -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION using 5000.0 points per unit in tabled values TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 726801 | TOTAL SIZE OF NONBOND LIST = 726801 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.2749E+04 1.4939E+01 4.2493E+01 O 2833 BOND = 0.0001 ANGLE = 0.0041 DIHED = 2.4829 VDWAALS = 1570.2522 EEL = -14304.7956 HBOND = 0.0000 1-4 VDW = 1.3654 1-4 EEL = -18.6616 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 50 -1.3231E+04 1.4136E+01 3.9686E+01 O 4108 BOND = 0.0650 ANGLE = 0.1616 DIHED = 2.5068 VDWAALS = 930.8503 EEL = -14146.0889 HBOND = 0.0000 1-4 VDW = 1.1157 1-4 EEL = -19.4429 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -1.3231E+04 1.4136E+01 3.9686E+01 O 4108 BOND = 0.0650 ANGLE = 0.1616 DIHED = 2.5068 VDWAALS = 930.8482 EEL = -14146.0855 HBOND = 0.0000 1-4 VDW = 1.1157 1-4 EEL = -19.4429 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 150 -1.3231E+04 1.4136E+01 3.9686E+01 O 4108 BOND = 0.0650 ANGLE = 0.1616 DIHED = 2.5068 VDWAALS = 930.8483 EEL = -14146.0835 HBOND = 0.0000 1-4 VDW = 1.1157 1-4 EEL = -19.4429 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -1.3231E+04 1.4136E+01 3.9686E+01 O 4108 BOND = 0.0650 ANGLE = 0.1616 DIHED = 2.5068 VDWAALS = 930.8461 EEL = -14146.0789 HBOND = 0.0000 1-4 VDW = 1.1157 1-4 EEL = -19.4429 RESTRAINT = 0.0000 .... RESTARTED DUE TO LINMIN FAILURE ... .... RESTARTED DUE TO LINMIN FAILURE ... NSTEP ENERGY RMS GMAX NAME NUMBER 250 -1.3231E+04 1.4136E+01 3.9686E+01 O 4108 BOND = 0.0650 ANGLE = 0.1616 DIHED = 2.5068 VDWAALS = 930.8455 EEL = -14146.0777 HBOND = 0.0000 1-4 VDW = 1.1157 1-4 EEL = -19.4429 RESTRAINT = 0.0000 .... RESTARTED DUE TO LINMIN FAILURE ... .... RESTARTED DUE TO LINMIN FAILURE ... NSTEP ENERGY RMS GMAX NAME NUMBER 300 -1.3231E+04 1.4136E+01 3.9686E+01 O 4108 BOND = 0.0650 ANGLE = 0.1616 DIHED = 2.5068 VDWAALS = 930.8448 EEL = -14146.0762 HBOND = 0.0000 1-4 VDW = 1.1157 1-4 EEL = -19.4429 RESTRAINT = 0.0000 .... RESTARTED DUE TO LINMIN FAILURE ... ***** REPEATED LINMIN FAILURE ***** ***** SEE http://amber.scripps.edu/Questions/linmin.html FOR MORE INFO ***** FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 314 -1.3231E+04 1.4136E+01 3.9686E+01 O 4108 BOND = 0.0650 ANGLE = 0.1616 DIHED = 2.5068 VDWAALS = 930.8446 EEL = -14146.0759 HBOND = 0.0000 1-4 VDW = 1.1157 1-4 EEL = -19.4429 RESTRAINT = 0.0000 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.01 ( 0.02% of Total) | Build the list 0.19 (66.07% of List ) | Other 0.10 (33.93% of List ) | List time 0.28 ( 0.42% of Nonbo) | Short_ene time 45.10 (98.71% of Direc) | Other 0.59 ( 1.29% of Direc) | Direct Ewald time 45.69 (68.76% of Ewald) | Adjust Ewald time 0.39 ( 0.59% of Ewald) | Fill Bspline coeffs 0.48 ( 2.36% of Recip) | Fill charge grid 1.87 ( 9.25% of Recip) | Scalar sum 3.11 (15.36% of Recip) | Grad sum 3.07 (15.14% of Recip) | FFT time 11.72 (57.87% of Recip) | Other 0.00 ( 0.02% of Recip) | Recip Ewald time 20.25 (30.47% of Ewald) | Virial junk 0.11 ( 0.17% of Ewald) | Ewald time 66.45 (99.58% of Nonbo) | Nonbond force 66.73 (100.0% of Force) | Bond/Angle/Dihedral 0.02 ( 0.03% of Force) | Other 0.03 ( 0.04% of Force) | Force time 66.78 (100.0% of Runmd) | Runmd Time 66.78 (98.79% of Total) | Other 0.80 ( 1.19% of Total) | Total time 67.60 (100.0% of ALL ) | Highest rstack allocated: 269948 | Highest istack allocated: 4578 | Job began at 14:36:40.741 on 04/22/2006 | Setup done at 14:36:41.077 on 04/22/2006 | Run done at 14:37:48.337 on 04/22/2006 | wallclock() was called 11942 times