------------------------------------------------------- Amber 12 SANDER 2012 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 11 | Run on 06/21/2011 at 09:27:33 | 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.pure_wat.CPU | INPCRD: eq1.x | PARM: prmtop | RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo Here is the input file: short md, nve ensemble &cntrl ntx=5, irest=1, ntc=2, ntf=2, tol=0.0000001, nstlim=10, ntt=0, ntpr=1, ntwr=10000, dt=0.001, / &ewald nfft1=60, 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 = 24.800 | 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 = 12288 NTYPES = 2 NBONH = 12288 MBONA = 0 NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0 NHPARM = 0 NPARM = 0 NNB = 16384 NRES = 4096 NBONA = 0 NTHETA = 0 NPHIA = 0 NUMBND = 2 NUMANG = 0 NPTRA = 0 NATYP = 2 NPHB = 1 IFBOX = 1 NMXRS = 3 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 11 11 11 | Direct force subcell size = 4.5091 4.5091 4.5091 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 5, 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 Molecular dynamics: nstlim = 10, 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 = 1 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 49.600 Box Y = 49.600 Box Z = 49.600 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 60 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 = 1.000 ps Number of triangulated 3-point waters found: 4096 Sum of charges from parm topology file = 0.00000000 Forcing neutrality... | Dynamic Memory, Types Used: | Reals 430124 | Integers 262151 | Nonbonded Pairs Initial Allocation: 2052403 -------------------------------------------------------------------------------- 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 = 1 TIME(PS) = 1.001 TEMP(K) = 298.28 PRESS = 0.0 Etot = -32059.9204 EKtot = 7282.8043 EPtot = -39342.7247 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6028.9517 EELEC = -45371.6764 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1767E-03 ------------------------------------------------------------------------------ NSTEP = 2 TIME(PS) = 1.002 TEMP(K) = 297.96 PRESS = 0.0 Etot = -32060.0178 EKtot = 7274.8748 EPtot = -39334.8926 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6029.7388 EELEC = -45364.6314 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1653E-03 ------------------------------------------------------------------------------ NSTEP = 3 TIME(PS) = 1.003 TEMP(K) = 297.71 PRESS = 0.0 Etot = -32059.9450 EKtot = 7268.8260 EPtot = -39328.7710 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6030.3442 EELEC = -45359.1152 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2153E-03 ------------------------------------------------------------------------------ NSTEP = 4 TIME(PS) = 1.004 TEMP(K) = 297.54 PRESS = 0.0 Etot = -32059.9269 EKtot = 7264.6265 EPtot = -39324.5534 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6030.8752 EELEC = -45355.4286 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2277E-03 ------------------------------------------------------------------------------ NSTEP = 5 TIME(PS) = 1.005 TEMP(K) = 297.44 PRESS = 0.0 Etot = -32060.0088 EKtot = 7262.1251 EPtot = -39322.1338 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6031.3191 EELEC = -45353.4529 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2122E-03 ------------------------------------------------------------------------------ NSTEP = 6 TIME(PS) = 1.006 TEMP(K) = 297.40 PRESS = 0.0 Etot = -32060.0152 EKtot = 7261.0867 EPtot = -39321.1019 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6031.7759 EELEC = -45352.8778 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2145E-03 ------------------------------------------------------------------------------ NSTEP = 7 TIME(PS) = 1.007 TEMP(K) = 297.40 PRESS = 0.0 Etot = -32060.1396 EKtot = 7261.2367 EPtot = -39321.3762 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6032.2790 EELEC = -45353.6552 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1652E-03 ------------------------------------------------------------------------------ NSTEP = 8 TIME(PS) = 1.008 TEMP(K) = 297.44 PRESS = 0.0 Etot = -32060.1101 EKtot = 7262.2977 EPtot = -39322.4078 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6032.7901 EELEC = -45355.1979 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1833E-03 ------------------------------------------------------------------------------ NSTEP = 9 TIME(PS) = 1.009 TEMP(K) = 297.51 PRESS = 0.0 Etot = -32060.1120 EKtot = 7264.0157 EPtot = -39324.1277 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6033.3461 EELEC = -45357.4737 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1900E-03 ------------------------------------------------------------------------------ NSTEP = 10 TIME(PS) = 1.010 TEMP(K) = 297.60 PRESS = 0.0 Etot = -32060.1148 EKtot = 7266.1795 EPtot = -39326.2943 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6033.9503 EELEC = -45360.2446 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1906E-03 ------------------------------------------------------------------------------ A V E R A G E S O V E R 10 S T E P S NSTEP = 10 TIME(PS) = 1.010 TEMP(K) = 297.63 PRESS = 0.0 Etot = -32060.0310 EKtot = 7266.8073 EPtot = -39326.8383 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6031.5370 EELEC = -45358.3754 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1941E-03 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 10 TIME(PS) = 1.010 TEMP(K) = 0.27 PRESS = 0.0 Etot = 0.0794 EKtot = 6.6635 EPtot = 6.6208 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 1.5199 EELEC = 5.6251 EHBOND = 0.0000 RESTRAINT = 0.0000 |E(PBS) = 0.0571 Ewald error estimate: 0.2108E-04 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 0.76 88.36 | Bond 0.00 0.00 | Angle 0.00 0.00 | Dihedral 0.00 0.00 | Shake 0.01 0.82 | RunMD 0.09 10.83 | Other 0.00 0.00 | ------------------------------ | Total 0.86 | PME Nonbond Pairlist CPU Time: | | Routine Sec % | --------------------------------- | Set Up Cit 0.00 0.00 | Build List 0.09 11.06 | --------------------------------- | Total 0.09 11.06 | PME Direct Force CPU Time: | | Routine Sec % | --------------------------------- | NonBonded Calc 0.48 56.46 | Exclude Masked 0.01 0.70 | Other 0.01 0.70 | --------------------------------- | Total 0.50 57.86 | PME Reciprocal Force CPU Time: | | Routine Sec % | --------------------------------- | 1D bspline 0.01 0.70 | Grid Charges 0.01 1.63 | Scalar Sum 0.03 3.73 | Gradient Sum 0.02 2.33 | FFT 0.09 11.06 | --------------------------------- | Total 0.17 19.44 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 9 steps: | Elapsed(s) = 0.81 Per Step(ms) = 89.56 | ns/day = 0.96 seconds/ns = 89559.76 | | Average timings for all steps: | Elapsed(s) = 0.99 Per Step(ms) = 98.59 | ns/day = 0.88 seconds/ns = 98589.40 | ----------------------------------------------------- | Setup CPU time: 0.12 seconds | NonSetup CPU time: 0.86 seconds | Total CPU time: 0.98 seconds 0.00 hours | Setup wall time: 0 seconds | NonSetup wall time: 1 seconds | Total wall time: 1 seconds 0.00 hours