------------------------------------------------------- Amber 12 SANDER 2012 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 11 | Run on 06/21/2011 at 09:23:34 | WARNING: Stack usage limited by a hard resource limit of 536870912 bytes! | If segment violations occur, get your sysadmin to increase the limit. [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: mdout.dhfr.min.CPU | INPCRD: md12.x | PARM: prmtop | RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo Here is the input file: short minimization &cntrl ntx=7, irest=1, ntc=2, ntf=2, tol=0.0000001, imin=1, maxcyc=5, ntpr=1, ntwr=10000, / &ewald nfft1 = 72, nfft2 = 60, nfft3 = 60, / | Conditional Compilation Defines Used: | DIRFRC_COMTRANS | DIRFRC_EFS | DIRFRC_NOVEC | PUBFFT | FFTLOADBAL_2PROC | BINTRAJ | MKL | Largest sphere to fit in unit cell has radius = 27.261 | INFO: Old style PARM file read | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting new box info from bottom of inpcrd NATOM = 22930 NTYPES = 17 NBONH = 21651 MBONA = 1302 NTHETH = 2789 MTHETA = 1772 NPHIH = 5026 MPHIA = 3140 NHPARM = 0 NPARM = 0 NNB = 41018 NRES = 6980 NBONA = 1302 NTHETA = 1772 NPHIA = 3140 NUMBND = 45 NUMANG = 91 NPTRA = 33 NATYP = 32 NPHB = 1 IFBOX = 1 NMXRS = 25 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 15 13 12 | Direct force subcell size = 4.6709 4.6571 4.5436 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 1, nmropt = 0 Nature and format of input: ntx = 7, irest = 1, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 10000 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 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 5, ncyc = 10, ntmin = 1 dx0 = 0.01000, drms = 0.00010 SHAKE: ntc = 2, jfastw = 0 tol = 0.00000 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 1 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 0 Box X = 70.063 Box Y = 60.543 Box Z = 54.523 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 72 NFFT2 = 60 NFFT3 = 60 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 = 510.050 ps Number of triangulated 3-point waters found: 6810 Sum of charges from parm topology file = -0.00000006 Forcing neutrality... | Dynamic Memory, Types Used: | Reals 629461 | Integers 698786 | Nonbonded Pairs Initial Allocation: 3829883 -------------------------------------------------------------------------------- 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 = 0.8332E-11 at 2.782960 --------------------------------------------------- |--------------------------------------------------- | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.47 | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.89 |--------------------------------------------------- NSTEP ENERGY RMS GMAX NAME NUMBER 1 -7.1862E+04 1.7352E+01 1.0607E+02 C 1855 BOND = 452.1694 ANGLE = 1277.0332 DIHED = 968.3542 VDWAALS = 8109.3884 EEL = -89881.5863 HBOND = 0.0000 1-4 VDW = 545.9443 1-4 EEL = 6666.3915 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 2 -7.1872E+04 1.7336E+01 1.0535E+02 C 1855 BOND = 448.4254 ANGLE = 1274.5367 DIHED = 968.0301 VDWAALS = 8106.9482 EEL = -89882.6104 HBOND = 0.0000 1-4 VDW = 545.8470 1-4 EEL = 6666.3611 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 3 -7.1885E+04 1.7318E+01 1.0448E+02 C 1855 BOND = 443.9987 ANGLE = 1271.5621 DIHED = 967.6423 VDWAALS = 8104.0209 EEL = -89883.8375 HBOND = 0.0000 1-4 VDW = 545.7307 1-4 EEL = 6666.3248 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 4 -7.1899E+04 1.7296E+01 1.0345E+02 C 1855 BOND = 438.7801 ANGLE = 1268.0227 DIHED = 967.1786 VDWAALS = 8100.5121 EEL = -89885.3006 HBOND = 0.0000 1-4 VDW = 545.5918 1-4 EEL = 6666.2814 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 5 -7.1916E+04 1.7270E+01 1.0223E+02 C 1855 BOND = 432.6501 ANGLE = 1263.8184 DIHED = 966.6244 VDWAALS = 8096.2934 EEL = -89887.0542 HBOND = 0.0000 1-4 VDW = 545.4260 1-4 EEL = 6666.2295 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 5 -7.1916E+04 1.7270E+01 1.0223E+02 C 1855 BOND = 432.6501 ANGLE = 1263.8184 DIHED = 966.6244 VDWAALS = 8096.2934 EEL = -89887.0542 HBOND = 0.0000 1-4 VDW = 545.4260 1-4 EEL = 6666.2295 RESTRAINT = 0.0000 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 0.67 84.32 | Bond 0.00 0.00 | Angle 0.00 0.38 | Dihedral 0.01 1.51 | Shake 0.01 0.88 | Other 0.10 12.92 | ------------------------------ | Total 0.80 | PME Nonbond Pairlist CPU Time: | | Routine Sec % | --------------------------------- | Set Up Cit 0.00 0.13 | Build List 0.09 11.54 | --------------------------------- | Total 0.09 11.67 | PME Direct Force CPU Time: | | Routine Sec % | --------------------------------- | NonBonded Calc 0.45 56.59 | Exclude Masked 0.01 1.25 | Other 0.00 0.63 | --------------------------------- | Total 0.47 58.47 | PME Reciprocal Force CPU Time: | | Routine Sec % | --------------------------------- | 1D bspline 0.01 1.00 | Grid Charges 0.01 1.63 | Scalar Sum 0.02 2.38 | Gradient Sum 0.02 2.13 | FFT 0.06 7.03 | --------------------------------- | Total 0.11 14.18 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 1 steps: | Elapsed(s) = 0.83 Per Step(ms) = 833.31 | ns/day = 0.10 seconds/ns = 833306.88 | | Average timings for all steps: | Elapsed(s) = 0.83 Per Step(ms) = 833.31 | ns/day = 0.10 seconds/ns = 833306.88 | ----------------------------------------------------- | Setup CPU time: 0.22 seconds | NonSetup CPU time: 0.80 seconds | Total CPU time: 1.01 seconds 0.00 hours | Setup wall time: 1 seconds | NonSetup wall time: 0 seconds | Total wall time: 1 seconds 0.00 hours