------------------------------------------------------- Amber 12 SANDER 2012 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 11 | Run on 06/21/2011 at 09:27:17 | 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.vrand.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=20, ntt=2, ntpr=1, ntwr=10000, dt=0.001, vrand=5, ntave=10, / &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 = 20, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00100, vlimit = 20.00000 Anderson (strong collision) temperature regulation: ig = 71277, vrand = 5 temp0 = 300.00000, tempi = 0.00000 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 ------------------------------------------------------------------------------ Setting new random velocities at step 5 NSTEP = 5 TIME(PS) = 1.005 TEMP(K) = 297.44 PRESS = 0.0 Etot = -32059.9269 EKtot = 7262.2069 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) = 298.66 PRESS = 0.0 Etot = -32030.2728 EKtot = 7291.8659 EPtot = -39322.1388 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6030.1423 EELEC = -45352.2811 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2253E-03 ------------------------------------------------------------------------------ NSTEP = 7 TIME(PS) = 1.007 TEMP(K) = 298.70 PRESS = 0.0 Etot = -32030.3166 EKtot = 7293.0192 EPtot = -39323.3359 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6028.4499 EELEC = -45351.7858 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2152E-03 ------------------------------------------------------------------------------ NSTEP = 8 TIME(PS) = 1.008 TEMP(K) = 298.78 PRESS = 0.0 Etot = -32030.3510 EKtot = 7295.0052 EPtot = -39325.3562 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6026.3658 EELEC = -45351.7220 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1954E-03 ------------------------------------------------------------------------------ NSTEP = 9 TIME(PS) = 1.009 TEMP(K) = 298.89 PRESS = 0.0 Etot = -32030.3210 EKtot = 7297.5436 EPtot = -39327.8646 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6023.8547 EELEC = -45351.7193 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2104E-03 ------------------------------------------------------------------------------ Setting new random velocities at step 10 NSTEP = 10 TIME(PS) = 1.010 TEMP(K) = 299.01 PRESS = 0.0 Etot = -32030.3210 EKtot = 7300.4481 EPtot = -39330.7691 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6020.9719 EELEC = -45351.7410 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1798E-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) = 298.30 PRESS = 0.0 Etot = -32045.1319 EKtot = 7283.1221 EPtot = -39328.2540 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6028.1014 EELEC = -45356.3554 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2023E-03 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 10 TIME(PS) = 1.010 TEMP(K) = 0.56 PRESS = 0.0 Etot = 14.8155 EKtot = 13.6960 EPtot = 6.1753 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 3.2038 EELEC = 6.4951 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2063E-04 ------------------------------------------------------------------------------ |=============================================================================== NSTEP = 11 TIME(PS) = 1.011 TEMP(K) = 297.91 PRESS = 0.0 Etot = -32054.4623 EKtot = 7273.6304 EPtot = -39328.0926 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6026.1102 EELEC = -45354.2029 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1821E-03 ------------------------------------------------------------------------------ NSTEP = 12 TIME(PS) = 1.012 TEMP(K) = 297.82 PRESS = 0.0 Etot = -32054.4749 EKtot = 7271.5572 EPtot = -39326.0321 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6030.9577 EELEC = -45356.9898 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1661E-03 ------------------------------------------------------------------------------ NSTEP = 13 TIME(PS) = 1.013 TEMP(K) = 297.76 PRESS = 0.0 Etot = -32054.4647 EKtot = 7270.0503 EPtot = -39324.5150 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6035.5544 EELEC = -45360.0694 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1613E-03 ------------------------------------------------------------------------------ NSTEP = 14 TIME(PS) = 1.014 TEMP(K) = 297.73 PRESS = 0.0 Etot = -32054.3774 EKtot = 7269.2110 EPtot = -39323.5884 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6039.9094 EELEC = -45363.4978 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1951E-03 ------------------------------------------------------------------------------ Setting new random velocities at step 15 NSTEP = 15 TIME(PS) = 1.015 TEMP(K) = 297.73 PRESS = 0.0 Etot = -32054.3774 EKtot = 7269.1830 EPtot = -39323.5603 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6044.1325 EELEC = -45367.6929 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1768E-03 ------------------------------------------------------------------------------ NSTEP = 16 TIME(PS) = 1.016 TEMP(K) = 301.45 PRESS = 0.0 Etot = -31966.1199 EKtot = 7359.9742 EPtot = -39326.0941 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6043.7534 EELEC = -45369.8474 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1727E-03 ------------------------------------------------------------------------------ NSTEP = 17 TIME(PS) = 1.017 TEMP(K) = 301.57 PRESS = 0.0 Etot = -31966.0694 EKtot = 7363.0445 EPtot = -39329.1139 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6043.7719 EELEC = -45372.8858 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1980E-03 ------------------------------------------------------------------------------ NSTEP = 18 TIME(PS) = 1.018 TEMP(K) = 301.71 PRESS = 0.0 Etot = -31966.0343 EKtot = 7366.5239 EPtot = -39332.5582 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6044.2107 EELEC = -45376.7689 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2049E-03 ------------------------------------------------------------------------------ NSTEP = 19 TIME(PS) = 1.019 TEMP(K) = 301.87 PRESS = 0.0 Etot = -31965.9593 EKtot = 7370.2337 EPtot = -39336.1930 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6044.9669 EELEC = -45381.1599 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2281E-03 ------------------------------------------------------------------------------ Setting new random velocities at step 20 NSTEP = 20 TIME(PS) = 1.020 TEMP(K) = 302.02 PRESS = 0.0 Etot = -31965.9593 EKtot = 7374.0015 EPtot = -39339.9609 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6045.9465 EELEC = -45385.9073 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2153E-03 ------------------------------------------------------------------------------ |=============================================================================== A V E R A G E S O V E R 10 S T E P S NSTEP = 20 TIME(PS) = 1.020 TEMP(K) = 299.76 PRESS = 0.0 Etot = -32010.2299 EKtot = 7318.7410 EPtot = -39328.9709 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6039.9313 EELEC = -45368.9022 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1900E-03 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 20 TIME(PS) = 1.020 TEMP(K) = 1.97 PRESS = 0.0 Etot = 44.2015 EKtot = 48.1588 EPtot = 5.3067 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6.4619 EELEC = 9.9234 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2081E-04 ------------------------------------------------------------------------------ |=============================================================================== A V E R A G E S O V E R 20 S T E P S NSTEP = 20 TIME(PS) = 1.020 TEMP(K) = 299.03 PRESS = 0.0 Etot = -32027.6809 EKtot = 7300.9315 EPtot = -39328.6124 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 6034.0164 EELEC = -45362.6288 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1962E-03 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 20 TIME(PS) = 1.020 TEMP(K) = 1.62 PRESS = 0.0 Etot = 37.2984 EKtot = 39.6308 EPtot = 5.7686 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 7.8101 EELEC = 10.4731 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2161E-04 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 1.41 91.81 | Bond 0.00 0.00 | Angle 0.00 0.00 | Dihedral 0.00 0.00 | Shake 0.01 0.85 | RunMD 0.11 7.35 | Other 0.00 0.00 | ------------------------------ | Total 1.54 | PME Nonbond Pairlist CPU Time: | | Routine Sec % | --------------------------------- | Set Up Cit 0.00 0.07 | Build List 0.09 6.18 | --------------------------------- | Total 0.10 6.24 | PME Direct Force CPU Time: | | Routine Sec % | --------------------------------- | NonBonded Calc 0.96 62.68 | Exclude Masked 0.01 0.78 | Other 0.01 0.46 | --------------------------------- | Total 0.98 63.91 | PME Reciprocal Force CPU Time: | | Routine Sec % | --------------------------------- | 1D bspline 0.01 0.65 | Grid Charges 0.03 2.15 | Scalar Sum 0.06 4.23 | Gradient Sum 0.04 2.60 | FFT 0.18 12.03 | --------------------------------- | Total 0.33 21.65 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 19 steps: | Elapsed(s) = 1.49 Per Step(ms) = 78.52 | ns/day = 1.10 seconds/ns = 78517.85 | | Average timings for all steps: | Elapsed(s) = 1.66 Per Step(ms) = 82.95 | ns/day = 1.04 seconds/ns = 82949.50 | ----------------------------------------------------- | Setup CPU time: 0.12 seconds | NonSetup CPU time: 1.54 seconds | Total CPU time: 1.65 seconds 0.00 hours | Setup wall time: 1 seconds | NonSetup wall time: 1 seconds | Total wall time: 2 seconds 0.00 hours