------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 01/12/2007 at 17:03:08 [-O]verwriting output File Assignments: | MDIN: sander.in | MDOUT: sander.out |INPCRD: parm.crd | PARM: parm.top |RESTRT: restrt.crd | REFC: refc.crd | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: !!! taup = 0.05 !!! &cntrl irest = 0, ntx = 1, ibelly = 0, ntr = 1, igb = 0, dielc = 1.0, cut = 12.0, imin = 1, maxcyc = 30, ntmin = 1, ncyc = 300, nstlim = 1, nsnb = 10, dt = 0.0010, t = 0, temp0 = 300.0, tempi = 150.0, ntt = 1, ntc = 2, nrespa = 1, ntb = 2, ntp = 1, pres0 = 1.0, taup = 0.2, iwrap = 1, ntpr = 1, ntwr = 100, ntwx = 100, &end Restrain of protein atoms 0.000 ATOM 1 END END -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: MPI getting new box info from bottom of inpcrd | peek_ewald_inpcrd: Box info found |Largest sphere to fit in unit cell has radius = 19.440 | New format PARM file being parsed. | Version = 1.000 Date = 01/12/07 Time = 16:29:27 NATOM = 6465 NTYPES = 2 NBONH = 3879 MBONA = 2586 NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0 NHPARM = 0 NPARM = 0 NNB = 14223 NRES = 1293 NBONA = 2586 NTHETA = 0 NPHIA = 0 NUMBND = 3 NUMANG = 0 NPTRA = 0 NATYP = 3 NPHB = 1 IFBOX = 1 NMXRS = 5 IFCAP = 0 NEXTRA = 2586 NCOPY = 0 | Memory Use Allocated | Real 644408 | Hollerith 40085 | Integer 441289 | Max Pairs 7095984 | Max Rstack 370390 | Max Istack 32325 | Total 37653 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- TP5 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 = 1, ntrx = 1, ntwr = 100 iwrap = 1, ntwx = 100, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 2, igb = 0, nsnb = 10 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 12.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 1 Energy minimization: maxcyc = 30, ncyc = 300, ntmin = 1 dx0 = 0.01000, drms = 0.00010 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 Extra-points options: frameon = 1, chngmask= 1 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 44.498 Box Y = 44.132 Box Z = 38.879 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 48 NFFT2 = 45 NFFT3 = 40 Cutoff= 12.000 Tol =0.100E-04 Ewald Coefficient = 0.22664 Interpolation order = 4 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES TP5 ----- READING GROUP 1; TITLE: Restrain of protein atoms GROUP 1 HAS HARMONIC CONSTRAINTS 0.00000 GROUP 1 CONSISTS OF ATOMS - 1 TO 1 Number of atoms in this group = 1 ----- END OF GROUP READ ----- | EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 3879 0 | EXTRA_PTS, trim_bonds: num bonds AFTER trim = 3879 0 | EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 2586 0 | EXTRA_PTS, trim_bonds: num bonds AFTER trim = 0 0 | EXTRA_PTS, trim_theta: num angle BEFORE trim = 0 0 | EXTRA_PTS, trim_theta: num angle AFTER trim = 0 0 | EXTRA_PTS, trim_theta: num angle BEFORE trim = 0 0 | EXTRA_PTS, trim_theta: num angle AFTER trim = 0 0 | EXTRA_PTS, trim_phi: num diheds BEFORE trim = 0 0 | EXTRA_PTS, trim_phi: num diheds AFTER trim = 0 0 | EXTRA_PTS, trim_phi: num diheds BEFORE trim = 0 0 | EXTRA_PTS, trim_phi: num diheds AFTER trim = 0 0 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- TP5 begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 1293 | Atom division among processors: | 0 6465 | Running AMBER/MPI version on 1 nodes 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 = 0.3338E-14 at 2.509280 | CHECK d/dx switch(x): max rel err = 0.8105E-11 at 2.712040 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 3110395 | TOTAL SIZE OF NONBOND LIST = 3110395 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.3251E+03 2.6217E+00 7.7667E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2125 EEL = -4581.8439 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 2 -5.3248E+03 2.6217E+00 7.7664E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2126 EEL = -4581.5758 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 3 -5.3248E+03 2.6217E+00 7.7663E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2126 EEL = -4581.6018 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 4 -5.3248E+03 2.6217E+00 7.7661E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2126 EEL = -4581.6329 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 5 -5.3249E+03 2.6217E+00 7.7659E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2126 EEL = -4581.6702 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 6 -5.3249E+03 2.6217E+00 7.7657E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2126 EEL = -4581.7150 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 7 -5.3250E+03 2.6217E+00 7.7654E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2126 EEL = -4581.7687 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 8 -5.3250E+03 2.6217E+00 7.7651E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2126 EEL = -4581.8330 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 9 -5.3251E+03 2.6218E+00 7.7647E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2126 EEL = -4581.9102 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 10 -5.3252E+03 2.6218E+00 7.7643E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2127 EEL = -4582.0028 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 11 -5.3253E+03 2.6218E+00 7.7638E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2127 EEL = -4582.1137 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 12 -5.3255E+03 2.6218E+00 7.7631E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2127 EEL = -4582.2466 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 13 -5.3256E+03 2.6218E+00 7.7623E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2128 EEL = -4582.4057 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 14 -5.3258E+03 2.6218E+00 7.7614E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2128 EEL = -4582.5963 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 15 -5.3260E+03 2.6218E+00 7.7603E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2129 EEL = -4582.8245 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 16 -5.3263E+03 2.6219E+00 7.7590E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2130 EEL = -4583.0970 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 17 -5.3266E+03 2.6219E+00 7.7575E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2131 EEL = -4583.4230 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 18 -5.3270E+03 2.6219E+00 7.7557E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2132 EEL = -4583.8121 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 19 -5.3275E+03 2.6220E+00 7.7536E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2133 EEL = -4584.2764 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 20 -5.3280E+03 2.6220E+00 7.7512E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2134 EEL = -4584.8302 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 21 -5.3287E+03 2.6221E+00 7.7483E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2136 EEL = -4585.4881 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 22 -5.3295E+03 2.6222E+00 7.7450E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2138 EEL = -4586.2689 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 23 -5.3304E+03 2.6223E+00 7.7412E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2141 EEL = -4587.1896 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 24 -5.3313E+03 2.6224E+00 7.7369E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2144 EEL = -4588.1066 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 25 -5.3324E+03 2.6226E+00 7.7322E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2147 EEL = -4589.1731 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 26 -5.3339E+03 2.6228E+00 7.7269E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2151 EEL = -4590.7041 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 27 -5.3357E+03 2.6230E+00 7.7213E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2156 EEL = -4592.5158 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 28 -5.3379E+03 2.6232E+00 7.7154E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2161 EEL = -4594.6441 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 29 -5.3403E+03 2.6235E+00 7.7096E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2163 EEL = -4597.1246 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 30 -5.3433E+03 2.6238E+00 7.7041E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2164 EEL = -4600.0395 HBOND = 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 30 -5.3433E+03 2.6238E+00 7.7041E+00 O 2456 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 VDWAALS = -743.2164 EEL = -4600.0395 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.03 ( 0.60% of Total) | Build the list 0.39 (92.21% of List ) | Other 0.03 ( 7.79% of List ) | List time 0.43 (11.79% of Nonbo) | Short_ene time 2.36 (99.33% of Direc) | Other 0.02 ( 0.67% of Direc) | Direct Ewald time 2.38 (74.54% of Ewald) | Adjust Ewald time 0.06 ( 1.85% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) | Fill Bspline coeffs 0.06 ( 8.23% of Recip) | Fill charge grid 0.18 (24.83% of Recip) | Scalar sum 0.06 ( 7.83% of Recip) | Grad sum 0.14 (19.00% of Recip) | FFT communication ti 0.00 ( 0.02% of FFT t) | Other 0.29 (100.0% of FFT t) | FFT time 0.29 (40.06% of Recip) | Other 0.00 ( 0.05% of Recip) | Recip Ewald time 0.72 (22.71% of Ewald) | Force Adjust 0.02 ( 0.53% of Ewald) | Virial junk 0.00 ( 0.07% of Ewald) | Start sycnronization 0.00 ( 0.01% of Ewald) | Other 0.01 ( 0.28% of Ewald) | Ewald time 3.19 (88.21% of Nonbo) | Nonbond force 3.61 (99.65% of Force) | Bond/Angle/Dihedral 0.01 ( 0.33% of Force) | Other 0.00 ( 0.02% of Force) | Force time 3.63 (100.0% of Runmd) | Runmd Time 3.63 (83.88% of Total) | Other 0.67 (15.52% of Total) | Total time 4.32 (100.0% of ALL ) | Highest rstack allocated: 364073 | Highest istack allocated: 6465 | Job began at 17:03:08.815 on 01/12/2007 | Setup done at 17:03:08.970 on 01/12/2007 | Run done at 17:03:13.139 on 01/12/2007 | wallclock() was called 1182 times