Log file opened on Tue Dec 16 15:10:10 2014 Host: etna.ii.uib.no pid: 7600 nodeid: 0 nnodes: 1 Gromacs version: VERSION 4.6.6 Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled GPU support: disabled invsqrt routine: gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library: fftpack (built-in) Large file support: enabled RDTSCP usage: enabled Built on: Wed Aug 13 11:30:34 CEST 2014 Built by: venken@etna.ii.uib.no [CMAKE] Build OS/arch: Linux 2.6.32-431.11.2.el6.x86_64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand: Intel(R) Xeon(R) CPU E5-2609 v2 @ 2.50GHz Build CPU family: 6 Model: 62 Stepping: 4 Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/cc GNU cc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) C compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -O3 -DNDEBUG :-) G R O M A C S (-: Gallium Rubidium Oxygen Manganese Argon Carbon Silicon :-) VERSION 4.6.6 (-: 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 = 50000 init-step = 0 cutoff-scheme = Group ns_type = Grid nstlist = 5 ndelta = 2 nstcomm = 100 comm-mode = Linear nstlog = 5000 nstxout = 500000 nstvout = 500000 nstfout = 500000 nstcalcenergy = 100 nstenergy = 5000 nstxtcout = 5000 init-t = 0 delta-t = 0.002 xtcprec = 1000 fourierspacing = 0.12 nkx = 56 nky = 56 nkz = 100 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 = V-rescale bPrintNHChains = FALSE nsttcouple = 5 epc = Berendsen epctype = Semiisotropic nstpcouple = 5 tau-p = 1 ref-p (3x3): ref-p[ 0]={ 1.01300e+00, 0.00000e+00, 0.00000e+00} ref-p[ 1]={ 0.00000e+00, 1.01300e+00, 0.00000e+00} ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.01300e+00} compress (3x3): compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-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 coulomb-modifier = None rcoulomb-switch = 0 rcoulomb = 1.2 vdwtype = Switch vdw-modifier = None rvdw-switch = 1.1 rvdw = 1.2 epsilon-r = 1 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: 628.982 35183 69070 ref-t: 310 310 310 tau-t: 0.1 0.1 0.1 anneal: No No No ann-npoints: 0 0 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 0 0 energygrp-flags[ 1]: 0 0 0 energygrp-flags[ 2]: 0 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 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: 0.419 nm, LJ-14, atoms 246 254 multi-body bonded interactions: 0.419 nm, Proper Dih., atoms 246 254 Minimum cell size due to bonded interactions: 0.461 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.819 nm Estimated maximum distance required for P-LINCS: 0.819 nm This distance will limit the DD cell size, you can override this with -rcon 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 1.024 nm The maximum allowed number of cells is: X 6 Y 6 Z 11 Domain decomposition grid 4 x 1 x 2, separate PME nodes 0 PME domain decomposition: 8 x 1 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) Xeon(R) CPU E5-2609 v2 @ 2.50GHz Family: 6 Model: 62 Stepping: 4 Features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb 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: FALSE 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 Using shifted Lennard-Jones, switch between 1.1 and 1.2 nm Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2 System total charge: 0.000 Generated table with 1100 data points for Ewald. Tabscale = 500 points/nm Generated table with 1100 data points for LJ6Switch. Tabscale = 500 points/nm Generated table with 1100 data points for LJ12Switch. Tabscale = 500 points/nm Generated table with 1100 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1100 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1100 data points for 1-4 LJ12. 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 Parallel 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 17959 There are inter charge-group constraints, will communicate selected coordinates each lincs iteration ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 -------- -------- --- Thank You --- -------- -------- Linking all bonded interactions to atoms There are 102713 inter charge-group exclusions, will use an extra communication step for exclusion forces for PME The initial number of communication pulses is: X 1 Z 1 The initial domain decomposition cell size is: X 1.62 nm Z 5.95 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) 1.200 nm atoms separated by up to 5 constraints (-rcon) 1.622 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 Z 1 The minimum size for domain decomposition cells is 1.200 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.74 Z 0.20 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) 1.200 nm atoms separated by up to 5 constraints (-rcon) 1.200 nm Making 2D domain decomposition grid 4 x 1 x 2, 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 ++++ G. Bussi, D. Donadio and M. Parrinello Canonical sampling through velocity rescaling J. Chem. Phys. 126 (2007) pp. 014101 -------- -------- --- Thank You --- -------- -------- There are: 52460 Atoms Charge group distribution at step 0: 3580 3762 3576 3770 3717 3766 3571 3694 Grid: 6 x 12 x 14 cells Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 1.44e-05 Initial temperature: 310.383 K Started mdrun on node 0 Thu Jan 1 01:00:00 1970 Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 3.01472e+04 3.50437e+04 1.05253e+02 -2.17953e+01 5.91881e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential -5.82465e+04 1.77724e+04 -5.68811e+05 -1.91628e+04 -5.57254e+05 Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd 1.35610e+05 -4.21645e+05 3.11016e+02 -5.97667e+03 2.53167e-05 DD step 4 load imb.: force 9.5% At step 500 the performance loss due to force load imbalance is 6.7 % NOTE: Turning on dynamic load balancing DD step 4999 vol min/aver 0.824 load imb.: force 3.3% Step Time Lambda 5000 10.00000 0.00000 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 4.50655e+04 3.30062e+04 2.88838e+02 -3.00416e-01 6.87201e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential -5.64105e+04 1.77376e+04 -4.96190e+05 -1.92388e+04 -4.68870e+05 Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd 1.33887e+05 -3.34983e+05 3.07065e+02 4.14686e+01 1.38854e-05 DD step 9999 vol min/aver 0.874 load imb.: force 0.5% Step Time Lambda 10000 20.00000 0.00000 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 4.51350e+04 3.23747e+04 3.07662e+02 -7.44927e+00 6.82460e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential -5.63941e+04 1.84603e+04 -4.99983e+05 -1.93224e+04 -4.72605e+05 Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd 1.35339e+05 -3.37266e+05 3.10395e+02 -7.63914e+01 1.44764e-05 DD step 14999 vol min/aver 0.857 load imb.: force 3.2% Step Time Lambda 15000 30.00000 0.00000 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 4.52095e+04 3.21773e+04 3.00856e+02 -3.40321e+00 6.72807e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential -5.61518e+04 1.78214e+04 -5.00986e+05 -1.93518e+04 -4.74256e+05 Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd 1.36188e+05 -3.38068e+05 3.12342e+02 -6.97267e+00 1.45728e-05 Writing checkpoint, step 15680 at Tue Dec 16 15:25:10 2014 DD step 19999 vol min/aver 0.872 load imb.: force 4.2% Step Time Lambda 20000 40.00000 0.00000 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 4.49540e+04 3.20943e+04 2.00425e+02 4.66420e+00 6.76742e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential -5.57284e+04 1.75130e+04 -5.00380e+05 -1.94929e+04 -4.74067e+05 Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd 1.34779e+05 -3.39288e+05 3.09112e+02 9.97339e+01 1.44570e-05 DD step 24999 vol min/aver 0.869 load imb.: force 4.0% Step Time Lambda 25000 50.00000 0.00000 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 4.51756e+04 3.19548e+04 3.12129e+02 4.82255e+00 6.62238e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential -5.52965e+04 1.65546e+04 -4.99122e+05 -1.96016e+04 -4.73396e+05 Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd 1.34350e+05 -3.39046e+05 3.08126e+02 -2.61753e+01 1.43118e-05 DD step 29999 vol min/aver 0.881 load imb.: force 2.3% Step Time Lambda 30000 60.00000 0.00000 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 4.49072e+04 3.18442e+04 3.15276e+02 -6.06507e+00 6.66214e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential -5.57564e+04 1.73473e+04 -5.01360e+05 -1.94517e+04 -4.75498e+05 Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd 1.35639e+05 -3.39859e+05 3.11083e+02 7.73554e+01 1.42209e-05 Writing checkpoint, step 31315 at Tue Dec 16 15:40:10 2014 DD step 34999 vol min/aver 0.921 load imb.: force 8.6% Step Time Lambda 35000 70.00000 0.00000 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 4.50212e+04 3.15945e+04 3.20599e+02 -1.19663e-01 6.62849e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential -5.59002e+04 1.84084e+04 -5.01793e+05 -1.95615e+04 -4.75281e+05 Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd 1.35050e+05 -3.40231e+05 3.09732e+02 1.23848e+02 1.40403e-05 DD step 39999 vol min/aver 0.873 load imb.: force 2.0% Step Time Lambda 40000 80.00000 0.00000 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 4.49917e+04 3.15589e+04 2.82528e+02 -1.32490e+01 6.64673e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential -5.54094e+04 1.81072e+04 -5.01871e+05 -1.95895e+04 -4.75296e+05 Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd 1.34655e+05 -3.40640e+05 3.08827e+02 1.53813e+02 1.49051e-05 DD step 44999 vol min/aver 0.968 load imb.: force 0.6% Step Time Lambda 45000 90.00000 0.00000 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 4.49817e+04 3.15803e+04 3.17471e+02 9.57291e+00 6.76483e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential -5.47926e+04 1.67757e+04 -4.99474e+05 -1.96982e+04 -4.73535e+05 Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd 1.34985e+05 -3.38550e+05 3.09584e+02 5.09446e+01 1.44293e-05 Writing checkpoint, step 47340 at Tue Dec 16 15:55:10 2014 DD step 49999 vol min/aver 0.984 load imb.: force 2.2% Step Time Lambda 50000 100.00000 0.00000 Writing checkpoint, step 50000 at Tue Dec 16 15:57:31 2014 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 4.58424e+04 3.16019e+04 2.85824e+02 1.03983e+01 6.62752e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential -5.47783e+04 1.86690e+04 -5.02865e+05 -1.97958e+04 -4.74403e+05 Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd 1.35256e+05 -3.39147e+05 3.10205e+02 1.79476e+02 1.47043e-05 <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 50001 steps using 501 frames Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 4.51591e+04 3.21527e+04 3.01285e+02 9.60726e-01 6.73034e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential -5.58031e+04 1.77071e+04 -5.00283e+05 -1.94625e+04 -4.73497e+05 Kinetic En. Total Energy Temperature Pressure (bar) Constr. rmsd 1.35059e+05 -3.38438e+05 3.09754e+02 -1.75525e+00 0.00000e+00 Box-X Box-Y Box-Z 6.52868e+00 6.52868e+00 1.19200e+01 Total Virial (kJ/mol) 4.47393e+04 1.42565e+02 2.58784e+01 1.42390e+02 4.49836e+04 -7.22216e+01 2.67413e+01 -7.23264e+01 4.54096e+04 Pressure (bar) -1.22624e+00 -1.05008e+01 -2.17709e+00 -1.04897e+01 -1.83366e+01 1.21305e+00 -2.23423e+00 1.21995e+00 1.42971e+01 Epot (kJ/mol) Coul-SR LJ-SR Coul-14 LJ-14 Protein-Protein -1.33134e+03 -3.63798e+02 5.71728e+03 4.39851e+02 Protein-Membrane -6.63230e+02 -6.35081e+02 0.00000e+00 0.00000e+00 Protein-rest -1.63387e+03 2.84617e+01 0.00000e+00 0.00000e+00 Membrane-Membrane 1.49360e+04 -2.64077e+04 -6.15204e+04 6.29049e+03 Membrane-rest -3.94370e+04 -4.63266e+03 0.00000e+00 0.00000e+00 rest-rest -4.72154e+05 4.97178e+04 0.00000e+00 0.00000e+00 T-Protein T-Membrane T-SOL 3.11102e+02 3.09908e+02 3.09663e+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] 7655.382168 7655.382 0.0 NB VdW [F] 501957.026434 501957.026 0.5 NB VdW & Elec. [V&F] 1179064.631648 1179064.632 1.2 NB VdW & Elec. [F] 81255230.506153 81255230.506 86.1 1,4 nonbonded interactions 2490.999819 224189.984 0.2 Calc Weights 7869.157380 283289.666 0.3 Spread Q Bspline 167875.357440 335750.715 0.4 Gather F Bspline 167875.357440 1007252.145 1.1 3D-FFT 572600.051772 4580800.414 4.9 Solve PME 156.803136 10035.401 0.0 NS-Pairs 179396.402008 3767324.442 4.0 Reset In Box 294.389436 883.168 0.0 CG-CoM 524.704920 1574.115 0.0 Propers 2986.909737 684002.330 0.7 Impropers 12.550251 2610.452 0.0 Virial 528.252820 9508.551 0.0 Stop-CM 26.334920 263.349 0.0 P-Coupling 2623.052460 15738.315 0.0 Calc-Ekin 1049.304920 28331.233 0.0 Lincs 1319.509020 79170.541 0.1 Lincs-Mat 30615.090444 122460.362 0.1 Constraint-V 4365.835008 34926.680 0.0 Constraint-Vir 609.306732 14623.362 0.0 Settle 575.634536 185929.955 0.2 (null) 0.850017 0.000 0.0 ----------------------------------------------------------------------------- Total 94332572.725 100.0 ----------------------------------------------------------------------------- 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 55898.3 av. #atoms communicated per step for LINCS: 2 x 8870.8 Average load imbalance: 3.1 % Part of the total run time spent waiting due to load imbalance: 1.5 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Z 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 % ----------------------------------------------------------------------------- Domain decomp. 8 1 10001 63.451 1265.957 2.2 DD comm. load 8 1 9906 0.808 16.127 0.0 DD comm. bounds 8 1 9901 1.356 27.052 0.0 Neighbor search 8 1 10001 483.035 9637.344 17.0 Comm. coord. 8 1 50001 11.301 225.468 0.4 Force 8 1 50001 1830.331 36518.147 64.4 Wait + Comm. F 8 1 50001 7.530 150.233 0.3 PME mesh 8 1 50001 363.301 7248.463 12.8 Write traj. 8 1 14 0.096 1.911 0.0 Update 8 1 50001 7.705 153.735 0.3 Constraints 8 1 50001 64.820 1293.270 2.3 Comm. energies 8 1 10001 2.568 51.238 0.1 Rest 8 5.146 102.667 0.2 ----------------------------------------------------------------------------- Total 8 2841.448 56691.611 100.0 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- PME redist. X/F 8 1 100002 157.155 3135.501 5.5 PME spread/gather 8 1 100002 81.846 1632.973 2.9 PME 3D-FFT 8 1 100002 91.973 1835.008 3.2 PME 3D-FFT Comm. 8 1 100002 23.844 475.720 0.8 PME solve 8 1 50001 8.328 166.160 0.3 ----------------------------------------------------------------------------- Core t (s) Wall t (s) (%) Time: 22083.050 2841.448 777.2 47:21 (ns/day) (hour/ns) Performance: 3.041 7.893 Finished mdrun on node 0 Tue Dec 16 15:57:32 2014