------------------------------------------------------- Amber 7 SANDER Scripps/UCSF 2002 ------------------------------------------------------- | Thu Jun 10 10:13:13 2004 [-O]verwriting output File Assignments: | MDIN: min.in | MDOUT: ttr_min_wat.out |INPCRD: ttr.crd | PARM: ttr.top |RESTRT: ttr_min.rst | REFC: ttr.rst | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Minimization with Cartesian restraints for the solute &cntrl imin=1, maxcyc=200, ntpr=5, ntr=1, &end Group input for restrained atoms 100.0 RES 1 458 END END -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: getting new box info from bottom of inpcrd | peek_ewald_inpcrd: Box info found | New format PARM file being parsed. | Version = 1.000 Date = 06/10/04 Time = 10:05:10 NATOM = 41630 NTYPES = 17 NBONH = 38070 MBONA = 3636 NTHETH = 7846 MTHETA = 4962 NPHIH = 14758 MPHIA = 9196 NHPARM = 0 NPARM = 0 NNB = 84884 NRES = 12012 NBONA = 3636 NTHETA = 4962 NPHIA = 9196 NUMBND = 45 NUMANG = 91 NPTRA = 40 NATYP = 32 NPHB = 1 IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0 | Memory Use Allocated Used | Real 6000000 3432451 | Hollerith 800000 261794 | Integer 6000000 3372863 | Max Nonbonded Pairs:10800000 | 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 = 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 = 1, igb = 0, nsnb = 25 ipol = 0, gbsa = 0 dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 1 Energy minimization: maxcyc = 200, ncyc = 10, ntmin = 1 dx0 = 0.01000, dxm = 0.50000, drms = 0.00010 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, frc_int = 0, netfrc = 1 Box X = 68.524 Box Y = 100.469 Box Z = 76.165 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 72 NFFT2 = 100 NFFT3 = 80 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES ----- READING GROUP 1; TITLE: Group input for restrained atoms GROUP 1 HAS HARMONIC CONSTRAINTS 100.00000 GRP 1 RES 1 TO 458 Number of atoms in this group = 7000 ----- END OF GROUP READ ----- -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 11538 Sum of charges from parm topology file = -0.00000020 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 = 0.3242E-14 at 2.436720 | CHECK d/dx switch(x): max rel err = 0.8156E-11 at 2.782960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 7046951 | TOTAL SIZE OF NONBOND LIST = 7046951 NSTEP ENERGY RMS GMAX NAME NUMBER 1 NAN NAN 6.4067E+04 C 6998 BOND = 4558117.5311 ANGLE = 1310.8486 DIHED = 3688.2075 VDWAALS = nan EEL = nan HBOND = 0.0000 1-4 VDW = 2028.5963 1-4 EEL = 22119.3049 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 5 NAN NAN 0.0000E+00 N 1 BOND = nan ANGLE = nan DIHED = nan VDWAALS = -1150.4840 EEL = nan HBOND = 0.0000 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = nan EAMBER = nan NSTEP ENERGY RMS GMAX NAME NUMBER 10 NAN NAN 0.0000E+00 N 1 BOND = nan ANGLE = nan DIHED = nan VDWAALS = -1150.4840 EEL = nan HBOND = 0.0000 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = nan EAMBER = nan .... RESTARTED DUE TO LINMIN FAILURE ... NSTEP ENERGY RMS GMAX NAME NUMBER 15 NAN NAN 0.0000E+00 N 1 BOND = nan ANGLE = nan DIHED = nan VDWAALS = -1150.4840 EEL = nan HBOND = 0.0000 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = nan EAMBER = nan .... RESTARTED DUE TO LINMIN FAILURE ... NSTEP ENERGY RMS GMAX NAME NUMBER 20 NAN NAN 0.0000E+00 N 1 BOND = nan ANGLE = nan DIHED = nan VDWAALS = -1150.4840 EEL = nan HBOND = 0.0000 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = nan EAMBER = nan .... RESTARTED DUE TO LINMIN FAILURE ... NSTEP ENERGY RMS GMAX NAME NUMBER 25 NAN NAN 0.0000E+00 N 1 BOND = nan ANGLE = nan DIHED = nan VDWAALS = -1150.4840 EEL = nan HBOND = 0.0000 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = nan EAMBER = nan .... RESTARTED DUE TO LINMIN FAILURE ... NSTEP ENERGY RMS GMAX NAME NUMBER 30 NAN NAN 0.0000E+00 N 1 BOND = nan ANGLE = nan DIHED = nan VDWAALS = -1150.4840 EEL = nan HBOND = 0.0000 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = nan EAMBER = nan .... RESTARTED DUE TO LINMIN FAILURE ... FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 31 NAN NAN 0.0000E+00 N 1 BOND = nan ANGLE = nan DIHED = nan VDWAALS = -1150.4840 EEL = nan HBOND = 0.0000 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = nan EAMBER = nan ***** REPEATED LINMIN FAILURE ***** -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.38 ( 0.03% of Total) | Ewald setup time 0.10 ( 0.44% of List ) | Check list validity 21.69 (96.02% of List ) | Map frac coords 0.01 ( 0.04% of List ) | Grid unit cell 0.04 ( 0.18% of List ) | Build the list 0.75 ( 3.32% of List ) | List time 22.59 ( 1.69% of Nonbo) | Direct Ewald time 685.61 (52.28% of Ewald) | Adjust Ewald time 46.87 ( 3.57% of Ewald) | Finish NB virial 17.41 ( 1.33% of Ewald) | Fill Bspline coeffs 54.37 ( 9.91% of Recip) | Fill charge grid 80.11 (14.61% of Recip) | Scalar sum 4.56 ( 0.83% of Recip) | Grad sum 405.15 (73.88% of Recip) | FFT time 4.21 ( 0.77% of Recip) | Recip Ewald time 548.40 (41.82% of Ewald) | Other 13.04 ( 0.99% of Ewald) | Ewald time 1311.33 (98.31% of Nonbo) | Nonbond force 1333.92 (94.70% of Force) | Bond energy 12.40 ( 0.88% of Force) | Angle energy 10.41 ( 0.74% of Force) | Dihedral energy 50.45 ( 3.58% of Force) | Other 1.43 ( 0.10% of Force) | Force time 1408.61 (100.0% of Runmd) | Runmd Time 1408.61 (98.16% of Total) | Other 26.00 ( 1.81% of Total) | Total time 1435.00 (100.0% of ALL ) | Highest rstack allocated: 2360268 | Highest istack allocated: 1562924 | Setup wallclock 9 seconds | Nonsetup wallclock 1451 seconds