------------------------------------------------------- Amber 12 SANDER 2012 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 11 | Run on 06/21/2011 at 15:04:58 | 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: jac.out | INPCRD: inpcrd.equil | PARM: prmtop | RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo Here is the input file: short md, jac, power 2 FFT &cntrl ntx=7, irest=1, ntc=2, ntf=2, tol=0.0000001, nstlim=20, ntpr=5, ntwr=10, dt=0.001, cut=9., ntt=0, temp0=300., / &ewald nfft1=64,nfft2=64,nfft3=64, / | Conditional Compilation Defines Used: | DIRFRC_COMTRANS | DIRFRC_EFS | DIRFRC_NOVEC | PUBFFT | FFTLOADBAL_2PROC | BINTRAJ | MKL | Largest sphere to fit in unit cell has radius = 31.115 | 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 = 23558 NTYPES = 16 NBONH = 22290 MBONA = 1302 NTHETH = 2789 MTHETA = 1772 NPHIH = 5026 MPHIA = 3140 NHPARM = 0 NPARM = 0 NNB = 41859 NRES = 7182 NBONA = 1302 NTHETA = 1772 NPHIA = 3140 NUMBND = 45 NUMANG = 91 NPTRA = 33 NATYP = 31 NPHB = 1 IFBOX = 1 NMXRS = 25 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 12 12 12 | Direct force subcell size = 5.1858 5.1858 5.1858 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 7, irest = 1, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 5, ntrx = 1, ntwr = 10 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 = 9.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 20, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00100, vlimit = 20.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00000 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 5 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 62.230 Box Y = 62.230 Box Z = 62.230 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 64 NFFT2 = 64 NFFT3 = 64 Cutoff= 9.000 Tol =0.100E-04 Ewald Coefficient = 0.30768 Interpolation order = 4 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 6.000 ps Number of triangulated 3-point waters found: 7023 Sum of charges from parm topology file = -11.00000006 Assuming uniform neutralizing plasma | Dynamic Memory, Types Used: | Reals 723509 | Integers 712219 | Nonbonded Pairs Initial Allocation: 5371224 -------------------------------------------------------------------------------- 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 --------------------------------------------------- |--------------------------------------------------- | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.39 | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.84 |--------------------------------------------------- NSTEP = 5 TIME(PS) = 6.005 TEMP(K) = 294.53 PRESS = 0.0 Etot = -58173.8279 EKtot = 14158.5058 EPtot = -72332.3337 BOND = 416.1874 ANGLE = 1127.5236 DIHED = 970.8642 1-4 NB = 545.0447 1-4 EEL = 6610.7410 VDWAALS = 8365.9923 EELEC = -90368.6870 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1488E-04 ------------------------------------------------------------------------------ NSTEP = 10 TIME(PS) = 6.010 TEMP(K) = 295.26 PRESS = 0.0 Etot = -58173.3549 EKtot = 14193.4601 EPtot = -72366.8149 BOND = 439.8346 ANGLE = 1150.7369 DIHED = 977.2061 1-4 NB = 543.3549 1-4 EEL = 6610.7282 VDWAALS = 8312.6506 EELEC = -90401.3261 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.4415E-04 ------------------------------------------------------------------------------ NSTEP = 15 TIME(PS) = 6.015 TEMP(K) = 296.86 PRESS = 0.0 Etot = -58173.8173 EKtot = 14270.2431 EPtot = -72444.0604 BOND = 441.2596 ANGLE = 1141.0062 DIHED = 976.3467 1-4 NB = 537.1377 1-4 EEL = 6602.1021 VDWAALS = 8261.6380 EELEC = -90403.5507 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.4481E-04 ------------------------------------------------------------------------------ NSTEP = 20 TIME(PS) = 6.020 TEMP(K) = 296.71 PRESS = 0.0 Etot = -58173.3622 EKtot = 14263.1568 EPtot = -72436.5190 BOND = 412.6438 ANGLE = 1170.7646 DIHED = 980.7194 1-4 NB = 538.6793 1-4 EEL = 6600.4972 VDWAALS = 8241.5797 EELEC = -90381.4030 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.4648E-04 ------------------------------------------------------------------------------ A V E R A G E S O V E R 4 S T E P S NSTEP = 20 TIME(PS) = 6.020 TEMP(K) = 295.84 PRESS = 0.0 Etot = -58173.5906 EKtot = 14221.3415 EPtot = -72394.9320 BOND = 427.4814 ANGLE = 1147.5079 DIHED = 976.2841 1-4 NB = 541.0541 1-4 EEL = 6606.0171 VDWAALS = 8295.4651 EELEC = -90388.7417 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.3758E-04 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 20 TIME(PS) = 6.020 TEMP(K) = 0.98 PRESS = 0.0 Etot = 0.2321 EKtot = 47.0786 EPtot = 47.0430 BOND = 13.1354 ANGLE = 15.7555 DIHED = 3.5320 1-4 NB = 3.2479 1-4 EEL = 4.7515 VDWAALS = 48.2632 EELEC = 14.4371 EHBOND = 0.0000 RESTRAINT = 0.0000 |E(PBS) = 0.0821 Ewald error estimate: 0.1313E-04 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 2.76 92.55 | Bond 0.00 0.00 | Angle 0.01 0.24 | Dihedral 0.02 0.84 | Shake 0.03 1.01 | RunMD 0.16 5.37 | Other 0.00 0.00 | ------------------------------ | Total 2.98 | PME Nonbond Pairlist CPU Time: | | Routine Sec % | --------------------------------- | Set Up Cit 0.00 0.10 | Build List 0.36 12.05 | --------------------------------- | Total 0.36 12.15 | PME Direct Force CPU Time: | | Routine Sec % | --------------------------------- | NonBonded Calc 1.85 62.07 | Exclude Masked 0.03 0.97 | Other 0.03 1.11 | --------------------------------- | Total 1.91 64.15 | PME Reciprocal Force CPU Time: | | Routine Sec % | --------------------------------- | 1D bspline 0.04 1.24 | Grid Charges 0.06 2.05 | Scalar Sum 0.07 2.25 | Gradient Sum 0.09 2.95 | FFT 0.23 7.75 | --------------------------------- | Total 0.48 16.25 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 15 steps: | Elapsed(s) = 3.60 Per Step(ms) = 239.82 | ns/day = 0.36 seconds/ns = 239822.40 | | Average timings for all steps: | Elapsed(s) = 4.38 Per Step(ms) = 219.02 | ns/day = 0.39 seconds/ns = 219020.95 | ----------------------------------------------------- | Setup CPU time: 0.11 seconds | NonSetup CPU time: 2.98 seconds | Total CPU time: 3.09 seconds 0.00 hours | Setup wall time: 0 seconds | NonSetup wall time: 4 seconds | Total wall time: 4 seconds 0.00 hours