Log file opened on Mon Mar 10 19:08:24 2014 Host: md74 pid: 7344 nodeid: 0 nnodes: 1 Gromacs version: VERSION 4.6.5 Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled GPU support: disabled invsqrt routine: gmx_software_invsqrt(x) CPU acceleration: SSE4.1 FFT library: fftw-3.3.2-sse2 Large file support: enabled RDTSCP usage: enabled Built on: Wed Dec 4 12:18:58 CET 2013 Built by: root@md74 [CMAKE] Build OS/arch: Linux 3.5.0-30-generic x86_64 Build CPU vendor: GenuineIntel Build CPU brand: Intel(R) Core(TM) i7 CPU 950 @ 3.07GHz Build CPU family: 6 Model: 26 Stepping: 5 Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 C compiler: /usr/bin/gcc GNU gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 C compiler flags: -msse4.1 -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG :-) G R O M A C S (-: Guyana Rwanda Oman Macau Angola Cameroon Senegal :-) 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 = md nsteps = 100000 init-step = 0 cutoff-scheme = Group ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 10 comm-mode = Linear nstlog = 10000 nstxout = 10000 nstvout = 10000 nstfout = 0 nstcalcenergy = 10 nstenergy = 10 nstxtcout = 100 init-t = 0 delta-t = 0.001 xtcprec = 1000 fourierspacing = 0.12 nkx = 32 nky = 32 nkz = 32 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 = Berendsen bPrintNHChains = FALSE nsttcouple = 10 epc = Berendsen epctype = Isotropic nstpcouple = 10 tau-p = 1 ref-p (3x3): ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} compress (3x3): compress[ 0]={ 5.00000e-05, 0.00000e+00, 0.00000e+00} compress[ 1]={ 0.00000e+00, 5.00000e-05, 0.00000e+00} compress[ 2]={ 0.00000e+00, 0.00000e+00, 5.00000e-05} 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 = 1.2 rlistlong = 1.2 nstcalclr = 0 rtpi = 0.05 coulombtype = PME-User coulomb-modifier = None rcoulomb-switch = 0 rcoulomb = 1.2 vdwtype = User vdw-modifier = None rvdw-switch = 0 rvdw = 1.2 epsilon-r = 2.5 epsilon-rf = 1 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 = 100 nbfgscorr = 10 ConstAlg = Lincs shake-tol = 0.0001 lincs-order = 4 lincs-warnangle = 30 lincs-iter = 8 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: 179.78 2272.22 ref-t: 298 298 tau-t: 0.1 0.1 anneal: No No ann-npoints: 0 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 2 0 energygrp-flags[ 1]: 0 2 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 Initializing Domain Decomposition on 8 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.446 nm, LJ-14, atoms 11 23 multi-body bonded interactions: 0.446 nm, Ryckaert-Bell., atoms 11 23 Minimum cell size due to bonded interactions: 0.490 nm Using 0 separate PME nodes, as there are too few total nodes for efficient splitting Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 8 cells with a minimum initial size of 0.613 nm The maximum allowed number of cells is: X 5 Y 5 Z 5 Domain decomposition grid 4 x 2 x 1, separate PME nodes 0 PME domain decomposition: 4 x 2 x 1 Domain decomposition nodeid 0, coordinates 0 0 0 Using 8 MPI threads Detecting CPU-specific acceleration. Present hardware specification: Vendor: GenuineIntel Brand: Intel(R) Core(TM) i7 CPU 950 @ 3.07GHz Family: 6 Model: 26 Stepping: 5 Features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 Acceleration most likely to fit this hardware: SSE4.1 Acceleration selected at GROMACS compile time: SSE4.1 Table routines are used for coulomb: TRUE Table routines are used for vdw: TRUE Will do PME sum in reciprocal space. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 -------- -------- --- Thank You --- -------- -------- Will do ordinary reciprocal space Ewald sum. Using a Gaussian width (1/beta) of 0.384195 nm for Ewald Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2 System total charge: -0.000 Read user tables from table.xvg with 1101 data points. Tabscale = 500 points/nm Modified table with 1100 data points for Ewald-User. Tabscale = 500 points/nm Read user tables from table_AA_AA.xvg with 1101 data points. Tabscale = 500 points/nm Modified table with 1100 data points for Ewald-User. Tabscale = 500 points/nm Read user tables from table_CG_CG.xvg with 1101 data points. Tabscale = 500 points/nm Modified table with 1100 data points for Ewald-User. Tabscale = 500 points/nm Read user tables from tablep.xvg with 1101 data points. Tabscale = 500 points/nm Potential shift: LJ r^-12: 0.000 r^-6 0.000, Ewald 0.000e+00 Initialized non-bonded Ewald correction tables, spacing: 7.23e-04 size: 3046 Removing pbc first time Pinning threads with an auto-selected logical core stride of 1 Initializing LINear Constraint Solver ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije LINCS: A Linear Constraint Solver for molecular simulations J. Comp. Chem. 18 (1997) pp. 1463-1472 -------- -------- --- Thank You --- -------- -------- The number of constraints is 650 Linking all bonded interactions to atoms There are 238 inter charge-group exclusions, will use an extra communication step for exclusion forces for PME-User There are 60 inter charge-group virtual sites, will an extra communication step for selected coordinates and forces The initial number of communication pulses is: X 2 Y 1 The initial domain decomposition cell size is: X 0.85 nm Y 1.71 nm The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.200 nm (the following are initial values, they could change due to box deformation) two-body bonded interactions (-rdd) 1.200 nm multi-body bonded interactions (-rdd) 0.853 nm virtual site constructions (-rcon) 0.853 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 2 Y 1 The minimum size for domain decomposition cells is 0.649 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.76 Y 0.70 The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.200 nm two-body bonded interactions (-rdd) 1.200 nm multi-body bonded interactions (-rdd) 0.649 nm virtual site constructions (-rcon) 0.649 nm Making 2D domain decomposition grid 4 x 2 x 1, home cell index 0 0 0 Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 (1984) pp. 3684-3690 -------- -------- --- Thank You --- -------- -------- There are: 1035 Atoms There are: 8 VSites Charge group distribution at step 0: 38 56 43 48 43 41 42 41 Grid: 5 x 4 x 3 cells Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 2.80e-07 Initial temperature: 0.000218527 K Started mdrun on node 0 Mon Mar 10 19:08:25 2014 Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) Bond Angle G96Angle Proper Dih. Ryckaert-Bell. 1.26077e+01 3.84070e+01 5.21364e-02 9.01182e-01 6.56255e+01 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 5.54289e+01 1.68738e+02 -7.38356e+03 -1.14543e+02 -2.45540e+02 Potential Kinetic En. Total Energy Temperature Pressure (bar) -7.40188e+03 3.36217e-01 -7.40154e+03 3.29831e-02 -1.13166e+03 Constr. rmsd 4.95626e-07 DD step 9 load imb.: force 88.3% At step 10 the performance loss due to force load imbalance is 13.7 % NOTE: Turning on dynamic load balancing DD load balancing is limited by minimum cell size in dimension X DD step 9999 vol min/aver 0.589! load imb.: force 27.8% Step Time Lambda 10000 10.00000 0.00000 Energies (kJ/mol) Bond Angle G96Angle Proper Dih. Ryckaert-Bell. 8.11932e+01 1.38529e+02 1.80675e+03 4.02664e+00 6.35349e+01 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 6.71576e+01 1.71812e+02 -7.29160e+03 -4.70463e+03 -1.43432e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -1.10975e+04 3.04813e+03 -8.04941e+03 2.99025e+02 -1.35389e+02 Constr. rmsd 5.99817e-07 DD load balancing is limited by minimum cell size in dimension X DD step 19999 vol min/aver 0.632! load imb.: force 25.6% Step Time Lambda 20000 20.00000 0.00000 Energies (kJ/mol) Bond Angle G96Angle Proper Dih. Ryckaert-Bell. 7.77290e+01 1.32659e+02 1.75463e+03 2.21520e+00 6.80437e+01 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 6.88350e+01 1.70696e+02 -7.22926e+03 -4.69431e+03 -1.43569e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -1.10845e+04 3.03282e+03 -8.05163e+03 2.97522e+02 4.99610e+02 Constr. rmsd 5.83737e-07 DD load balancing is limited by minimum cell size in dimension X DD step 29999 vol min/aver 0.663! load imb.: force 26.8% Step Time Lambda 30000 30.00000 0.00000 Energies (kJ/mol) Bond Angle G96Angle Proper Dih. Ryckaert-Bell. 7.09588e+01 1.37595e+02 1.75452e+03 4.29699e+00 5.64469e+01 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 6.63958e+01 1.70277e+02 -7.30681e+03 -4.65354e+03 -1.43995e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -1.11398e+04 3.03803e+03 -8.10179e+03 2.98033e+02 1.44851e+02 Constr. rmsd 5.73459e-07 DD load balancing is limited by minimum cell size in dimension X DD step 39999 vol min/aver 0.615! load imb.: force 49.9% Step Time Lambda 40000 40.00000 0.00000 Energies (kJ/mol) Bond Angle G96Angle Proper Dih. Ryckaert-Bell. 1.05682e+02 1.46114e+02 1.75519e+03 4.96164e+00 7.15563e+01 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 5.56032e+01 1.68212e+02 -7.36767e+03 -4.54353e+03 -1.42731e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -1.10312e+04 3.03544e+03 -7.99575e+03 2.97779e+02 2.22725e+02 Constr. rmsd 5.82589e-07 DD load balancing is limited by minimum cell size in dimension X DD step 49999 vol min/aver 0.603! load imb.: force 35.1% Step Time Lambda 50000 50.00000 0.00000 Energies (kJ/mol) Bond Angle G96Angle Proper Dih. Ryckaert-Bell. 1.20135e+02 1.28369e+02 1.74440e+03 3.50227e+00 6.44520e+01 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 5.81577e+01 1.64302e+02 -7.46672e+03 -4.72209e+03 -1.42069e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -1.13262e+04 3.03061e+03 -8.29556e+03 2.97306e+02 -3.34407e+02 Constr. rmsd 5.99494e-07 DD load balancing is limited by minimum cell size in dimension X DD step 59999 vol min/aver 0.614! load imb.: force 30.2% Step Time Lambda 60000 60.00000 0.00000 Energies (kJ/mol) Bond Angle G96Angle Proper Dih. Ryckaert-Bell. 8.77442e+01 1.45227e+02 1.76874e+03 2.33343e+01 8.19118e+01 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 6.23344e+01 1.71225e+02 -7.46426e+03 -4.60630e+03 -1.41508e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -1.11451e+04 3.06957e+03 -8.07554e+03 3.01128e+02 -3.30595e+02 Constr. rmsd 5.44462e-07 DD load balancing is limited by minimum cell size in dimension X DD step 69999 vol min/aver 0.638! load imb.: force 28.1% Step Time Lambda 70000 70.00000 0.00000 Energies (kJ/mol) Bond Angle G96Angle Proper Dih. Ryckaert-Bell. 6.92646e+01 1.45322e+02 1.80140e+03 3.39157e+00 6.56844e+01 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 6.75610e+01 1.67717e+02 -7.40467e+03 -4.68973e+03 -1.40892e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -1.11830e+04 3.00401e+03 -8.17896e+03 2.94696e+02 2.84314e+01 Constr. rmsd 6.25397e-07 DD load balancing is limited by minimum cell size in dimension X DD step 79999 vol min/aver 0.668! load imb.: force 15.2% Step Time Lambda 80000 80.00000 0.00000 Energies (kJ/mol) Bond Angle G96Angle Proper Dih. Ryckaert-Bell. 8.47827e+01 1.53695e+02 1.73728e+03 1.37138e+01 6.93882e+01 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 6.68032e+01 1.63777e+02 -7.37339e+03 -4.58020e+03 -1.39520e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -1.10594e+04 2.98768e+03 -8.07168e+03 2.93094e+02 2.87947e+02 Constr. rmsd 5.49622e-07 DD load balancing is limited by minimum cell size in dimension X DD step 89999 vol min/aver 0.695! load imb.: force 22.5% Step Time Lambda 90000 90.00000 0.00000 Energies (kJ/mol) Bond Angle G96Angle Proper Dih. Ryckaert-Bell. 8.28355e+01 1.15117e+02 1.73338e+03 7.57591e+00 6.63817e+01 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 6.38273e+01 1.67987e+02 -7.18913e+03 -4.63425e+03 -1.40704e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -1.09933e+04 2.94296e+03 -8.05036e+03 2.88707e+02 2.27488e+02 Constr. rmsd 5.47280e-07 DD load balancing is limited by minimum cell size in dimension X DD step 99999 vol min/aver 0.714! load imb.: force 34.6% Step Time Lambda 100000 100.00000 0.00000 Writing checkpoint, step 100000 at Mon Mar 10 19:09:31 2014 Energies (kJ/mol) Bond Angle G96Angle Proper Dih. Ryckaert-Bell. 7.13726e+01 1.28125e+02 1.77982e+03 4.18186e+00 6.82299e+01 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 7.37656e+01 1.65367e+02 -7.45581e+03 -4.59759e+03 -1.41240e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -1.11749e+04 3.08899e+03 -8.08595e+03 3.03032e+02 1.43798e+02 Constr. rmsd 5.80380e-07 <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 100001 steps using 10001 frames Energies (kJ/mol) Bond Angle G96Angle Proper Dih. Ryckaert-Bell. 8.41668e+01 1.30696e+02 1.77404e+03 6.53182e+00 7.19037e+01 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 6.32086e+01 1.66751e+02 -7.33032e+03 -4.65159e+03 -1.42127e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -1.11059e+04 3.05301e+03 -8.05288e+03 2.99502e+02 -2.26929e+01 Constr. rmsd 0.00000e+00 Box-X Box-Y Box-Z 3.28230e+00 3.28230e+00 3.28230e+00 Total Virial (kJ/mol) 1.43313e+03 -1.21732e+02 6.79049e+02 -1.21732e+02 5.59777e+02 -1.44153e+02 6.79049e+02 -1.44153e+02 1.13708e+03 Pressure (bar) -4.92327e+02 1.48821e+02 -8.02179e+02 1.48821e+02 5.39664e+02 1.62917e+02 -8.02179e+02 1.62917e+02 -1.15415e+02 Epot (kJ/mol) Coul-SR LJ-SR Coul-14 LJ-14 AA-AA -8.97578e+01 -3.04407e+01 1.66751e+02 6.32086e+01 AA-CG -3.57441e+01 0.00000e+00 0.00000e+00 0.00000e+00 CG-CG -4.52609e+03 -7.29988e+03 0.00000e+00 0.00000e+00 T-AA T-CG 3.17620e+02 2.98069e+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] 9468.753802 9468.754 0.8 NB VdW [F] 73249.273368 73249.273 6.1 NB Elec. [V&F] 22684.119072 22684.119 1.9 NB Elec. [F] 185532.628788 185532.629 15.6 NB VdW & Elec. [V&F] 995.700461 995.700 0.1 NB VdW & Elec. [F] 7504.246359 7504.246 0.6 1,4 nonbonded interactions 14.500145 1305.013 0.1 Calc Weights 312.903129 11264.513 0.9 Spread Q Bspline 6675.266752 13350.534 1.1 Gather F Bspline 6675.266752 40051.601 3.4 3D-FFT 98304.983040 786439.864 66.0 Solve PME 204.802048 13107.331 1.1 NS-Pairs 407.175562 8550.687 0.7 Reset In Box 3.520352 10.561 0.0 CG-CoM 10.432086 31.296 0.0 Bonds 5.900059 348.103 0.0 Angles 43.300433 7274.473 0.6 Propers 0.800008 183.202 0.0 RB-Dihedrals 11.200112 2766.428 0.2 Virial 14.031403 252.565 0.0 Stop-CM 10.432086 104.321 0.0 P-Coupling 104.301043 625.806 0.1 Calc-Ekin 20.862086 563.276 0.0 Lincs 65.001950 3900.117 0.3 Lincs-Mat 390.011700 1560.047 0.1 Constraint-V 130.002600 1040.021 0.1 Constraint-Vir 6.500650 156.016 0.0 Virtual Site N 6.600120 99.002 0.0 ----------------------------------------------------------------------------- Total 1192419.497 100.0 ----------------------------------------------------------------------------- D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 3236.9 av. #atoms communicated per step for vsites: 3 x 15.4 Average load imbalance: 28.7 % Part of the total run time spent waiting due to load imbalance: 7.0 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 9 % Y 0 % NOTE: 7.0 % of the available CPU time was lost due to load imbalance in the domain decomposition. 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 % ----------------------------------------------------------------------------- Domain decomp. 8 1 10001 1.770 44.016 2.7 DD comm. load 8 1 10000 0.058 1.442 0.1 DD comm. bounds 8 1 10000 0.156 3.887 0.2 Vsite constr. 8 1 100001 0.559 13.904 0.8 Neighbor search 8 1 10001 3.209 79.785 4.8 Comm. coord. 8 1 100001 2.031 50.486 3.0 Force 8 1 100001 18.049 448.768 27.1 Wait + Comm. F 8 1 100001 1.036 25.760 1.6 PME mesh 8 1 100001 31.840 791.665 47.8 Vsite spread 8 1 110002 0.387 9.617 0.6 Write traj. 8 1 1001 0.037 0.923 0.1 Update 8 1 100001 0.576 14.310 0.9 Constraints 8 1 100001 5.512 137.040 8.3 Comm. energies 8 1 10001 0.339 8.436 0.5 Rest 8 1.022 25.403 1.5 ----------------------------------------------------------------------------- Total 8 66.581 1655.443 100.0 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- PME redist. X/F 8 1 200002 8.948 222.490 13.4 PME spread/gather 8 1 200002 7.514 186.819 11.3 PME 3D-FFT 8 1 200002 9.314 231.570 14.0 PME 3D-FFT Comm. 8 1 400004 3.023 75.165 4.5 PME solve 8 1 100001 2.863 71.181 4.3 ----------------------------------------------------------------------------- Core t (s) Wall t (s) (%) Time: 528.090 66.581 793.2 (ns/day) (hour/ns) Performance: 129.768 0.185 Finished mdrun on node 0 Mon Mar 10 19:09:31 2014