Log file opened on Fri Nov 7 18:09:55 2014 Host: Labtop.local pid: 2929 nodeid: 0 nnodes: 1 Gromacs version: VERSION 4.6.5 Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP support: disabled GPU support: disabled invsqrt routine: gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library: fftw-3.3.3 Large file support: enabled RDTSCP usage: enabled Built on: Mon Feb 24 16:07:01 CET 2014 Built by: tom@Labtop.local [CMAKE] Build OS/arch: Darwin 13.0.0 x86_64 Build CPU vendor: GenuineIntel Build CPU brand: Intel(R) Core(TM) i7-3720QM CPU @ 2.60GHz Build CPU family: 6 Model: 58 Stepping: 9 Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/cc Clang Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) C compiler flags: -mavx -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas -O3 -DNDEBUG :-) G R O M A C S (-: Giant Rising Ordinary Mutants for A Clerical Setup :-) VERSION 4.6.5 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) mdrun (-: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 -------- -------- --- Thank You --- -------- -------- Input Parameters: integrator = steep nsteps = 10 init-step = 0 cutoff-scheme = Group ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 100 comm-mode = Linear nstlog = 100 nstxout = 0 nstvout = 0 nstfout = 0 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 init-t = 0 delta-t = 0.02 xtcprec = 10 fourierspacing = 0.12 nkx = 0 nky = 0 nkz = 0 pme-order = 4 ewald-rtol = 1e-05 ewald-geometry = 0 epsilon-surface = 0 optimize-fft = FALSE ePBC = xyz bPeriodicMols = FALSE bContinuation = FALSE bShakeSOR = FALSE etc = No bPrintNHChains = FALSE nsttcouple = -1 epc = No epctype = Isotropic nstpcouple = -1 tau-p = 1 ref-p (3x3): ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress (3x3): compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} refcoord-scaling = No posres-com (3): posres-com[0]= 0.00000e+00 posres-com[1]= 0.00000e+00 posres-com[2]= 0.00000e+00 posres-comB (3): posres-comB[0]= 0.00000e+00 posres-comB[1]= 0.00000e+00 posres-comB[2]= 0.00000e+00 verlet-buffer-drift = 0.005 rlist = 1.4 rlistlong = 1.4 nstcalclr = 0 rtpi = 0.05 coulombtype = Shift coulomb-modifier = None rcoulomb-switch = 0 rcoulomb = 1.2 vdwtype = Shift vdw-modifier = None rvdw-switch = 0.9 rvdw = 1.2 epsilon-r = 15 epsilon-rf = inf tabext = 1 implicit-solvent = No gb-algorithm = Still gb-epsilon-solvent = 80 nstgbradii = 1 rgbradii = 1 gb-saltconc = 0 gb-obc-alpha = 1 gb-obc-beta = 0.8 gb-obc-gamma = 4.85 gb-dielectric-offset = 0.009 sa-algorithm = Ace-approximation sa-surface-tension = 2.05016 DispCorr = No bSimTemp = FALSE free-energy = no nwall = 0 wall-type = 9-3 wall-atomtype[0] = -1 wall-atomtype[1] = -1 wall-density[0] = 0 wall-density[1] = 0 wall-ewald-zfac = 3 pull = no rotation = FALSE disre = No disre-weighting = Conservative disre-mixed = FALSE dr-fc = 1000 dr-tau = 0 nstdisreout = 100 orires-fc = 0 orires-tau = 0 nstorireout = 100 dihre-fc = 0 em-stepsize = 0.01 em-tol = 10 niter = 20 fc-stepsize = 0 nstcgsteep = 1000 nbfgscorr = 10 ConstAlg = Lincs shake-tol = 0.0001 lincs-order = 4 lincs-warnangle = 30 lincs-iter = 1 bd-fric = 0 ld-seed = 1993 cos-accel = 0 deform (3x3): deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} adress = FALSE userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 grpopts: nrdf: 183 ref-t: 0 tau-t: 0 anneal: No ann-npoints: 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 efield-x: n = 0 efield-xt: n = 0 efield-y: n = 0 efield-yt: n = 0 efield-z: n = 0 efield-zt: n = 0 bQMMM = FALSE QMconstraints = 0 QMMMscheme = 0 scalefactor = 1 qm-opts: ngQM = 0 Using 1 MPI thread Detecting CPU-specific acceleration. Present hardware specification: Vendor: GenuineIntel Brand: Intel(R) Core(TM) i7-3720QM CPU @ 2.60GHz Family: 6 Model: 58 Stepping: 9 Features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic Acceleration most likely to fit this hardware: AVX_256 Acceleration selected at GROMACS compile time: AVX_256 Table routines are used for coulomb: TRUE Table routines are used for vdw: TRUE Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm Cut-off's: NS: 1.4 Coulomb: 1.2 LJ: 1.2 System total charge: 0.000 Generated table with 1200 data points for Shift. Tabscale = 500 points/nm Generated table with 1200 data points for LJ6Shift. Tabscale = 500 points/nm Generated table with 1200 data points for LJ12Shift. Tabscale = 500 points/nm Potential shift: LJ r^-12: 0.000 r^-6 0.000 Removing pbc first time Initializing LINear Constraint Solver ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess P-LINCS: A Parallel Linear Constraint Solver for molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 116-122 -------- -------- --- Thank You --- -------- -------- The number of constraints is 63 17 constraints are involved in constraint triangles, will apply an additional matrix expansion of order 4 for couplings between constraints inside triangles Initiating Steepest Descents Max number of connections per atom is 19 Total number of connections is 664 Max number of graph edges per atom is 3 Total number of graph edges is 188 Rel. Constraint Deviation: RMS MAX between atoms Before LINCS 0.400950 0.900368 48 49 After LINCS 0.000659 0.004029 87 88 Started Steepest Descents on node 0 Fri Nov 7 18:09:55 2014 Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 10 Grid: 5 x 5 x 5 cells Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 4.22950e+01 1.94163e+02 1.79809e+01 6.37016e+00 1.43656e+03 Coulomb (SR) Potential Pressure (bar) Constr. rmsd -3.84591e+00 1.69352e+03 5.77188e+01 6.58807e-04 Step Time Lambda 1 1.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 4.07139e+01 1.90485e+02 1.81919e+01 6.50639e+00 8.68582e+02 Coulomb (SR) Potential Pressure (bar) Constr. rmsd -3.85434e+00 1.12063e+03 2.38322e+01 1.81066e-06 Step Time Lambda 2 2.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 3.90489e+01 1.88116e+02 2.37027e+01 6.75836e+00 3.68560e+02 Coulomb (SR) Potential Pressure (bar) Constr. rmsd -3.87299e+00 6.22313e+02 -3.35825e+00 2.74030e-06 Step Time Lambda 3 3.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 3.69787e+01 1.84632e+02 3.49377e+01 7.16662e+00 -5.51285e+01 Coulomb (SR) Potential Pressure (bar) Constr. rmsd -3.90633e+00 2.04681e+02 -2.34627e+01 4.32262e-06 Step Time Lambda 4 4.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 3.32334e+01 1.66418e+02 3.59912e+01 7.65331e+00 -3.75780e+02 Coulomb (SR) Potential Pressure (bar) Constr. rmsd -3.95434e+00 -1.36438e+02 -3.45766e+01 6.62265e-06 Step Time Lambda 5 5.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 2.63560e+01 1.40974e+02 1.66493e+01 7.92130e+00 -5.36391e+02 Coulomb (SR) Potential Pressure (bar) Constr. rmsd -3.98887e+00 -3.48479e+02 -3.64535e+01 1.82577e-05 Step Time Lambda 6 6.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 1.67924e+01 1.25282e+02 2.16769e+01 8.34986e+00 -6.61440e+02 Coulomb (SR) Potential Pressure (bar) Constr. rmsd -4.03416e+00 -4.93373e+02 -4.17667e+01 8.36971e-06 Step Time Lambda 7 7.00000 0.00000 Step Time Lambda 8 8.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 1.41275e+01 1.14653e+02 1.62281e+01 8.08771e+00 -6.78283e+02 Coulomb (SR) Potential Pressure (bar) Constr. rmsd -4.06776e+00 -5.29254e+02 -3.75595e+01 1.98645e-05 Step Time Lambda 9 9.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 1.14065e+01 1.11948e+02 2.55676e+01 8.42866e+00 -7.08788e+02 Coulomb (SR) Potential Pressure (bar) Constr. rmsd -4.08864e+00 -5.55525e+02 -4.20103e+01 1.86245e-05 Step Time Lambda 10 10.00000 0.00000 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. Steepest Descents did not converge to Fmax < 10 in 11 steps. Potential Energy = -5.5552533e+02 Maximum force = 4.8559814e+02 on atom 54 Norm of force = 1.9879941e+02 M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) V&F=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops ----------------------------------------------------------------------------- NB VdW [V&F] 0.810609 0.811 40.5 NB Elec. [V&F] 0.092136 0.092 4.6 NS-Pairs 0.031710 0.666 33.3 Reset In Box 0.000979 0.003 0.1 Shift-X 0.000979 0.006 0.3 CG-CoM 0.000979 0.003 0.1 Bonds 0.000275 0.016 0.8 Angles 0.000748 0.126 6.3 Propers 0.000286 0.065 3.3 Impropers 0.000066 0.014 0.7 Virial 0.001474 0.027 1.3 Lincs 0.001386 0.083 4.2 Lincs-Mat 0.018216 0.073 3.6 Constraint-Vir 0.000693 0.017 0.8 Virtual Site 2 0.000066 0.002 0.1 ----------------------------------------------------------------------------- Total 2.002 100.0 ----------------------------------------------------------------------------- R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Th. Count Wall t (s) G-Cycles % ----------------------------------------------------------------------------- Neighbor search 1 1 11 0.001 0.003 20.2 Force 1 1 11 0.000 0.001 6.5 Vsite spread 1 1 11 0.000 0.000 0.2 Constraints 1 1 21 0.000 0.000 2.3 Rest 1 0.002 0.011 70.8 ----------------------------------------------------------------------------- Total 1 0.003 0.016 100.0 ----------------------------------------------------------------------------- Core t (s) Wall t (s) (%) Time: 0.003 0.003 100.0 (steps/hour) Performance: 12716824.0 Finished mdrun on node 0 Fri Nov 7 18:09:55 2014