Log file opened on Thu Mar 10 16:10:49 2016 Host: etna.ii.uib.no pid: 7318 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 Feb 3 15:53:35 CET 2016 Built by: venken@etna.ii.uib.no [CMAKE] Build OS/arch: Linux 2.6.32-504.3.3.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 4.4.7-11) 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 (-: GROup of MAchos and Cynical Suckers :-) 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 = 2500000 init-step = 0 cutoff-scheme = Group ns_type = Grid nstlist = 5 ndelta = 2 nstcomm = 100 comm-mode = Linear nstlog = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 5000 init-t = 0 delta-t = 0.02 xtcprec = 1000 fourierspacing = 0.12 nkx = 80 nky = 80 nkz = 80 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 = Parrinello-Rahman epctype = Isotropic nstpcouple = 5 tau-p = 12 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]={ 3.00000e-04, 0.00000e+00, 0.00000e+00} compress[ 1]={ 0.00000e+00, 3.00000e-04, 0.00000e+00} compress[ 2]={ 0.00000e+00, 0.00000e+00, 3.00000e-04} refcoord-scaling = All 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 = Shift vdw-modifier = None rvdw-switch = 0.9 rvdw = 1.2 epsilon-r = 2.5 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: 102.98 4991.04 10494 ref-t: 320 320 320 tau-t: 1 1 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: 0.528 nm, Bond, atoms 518 519 multi-body bonded interactions: 0.983 nm, G96Angle, atoms 129 136 Minimum cell size due to bonded interactions: 1.081 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 1.550 nm Estimated maximum distance required for P-LINCS: 1.550 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 1.937 nm The maximum allowed number of cells is: X 4 Y 4 Z 4 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) 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 0.9 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 LJ6Shift. Tabscale = 500 points/nm Generated table with 1100 data points for LJ12Shift. 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 3030 There are inter charge-group constraints, will communicate selected coordinates each lincs iteration 6 constraints are involved in constraint triangles, will apply an additional matrix expansion of order 4 for couplings between constraints inside triangles Linking all bonded interactions to atoms There are 1583 inter charge-group exclusions, will use an extra communication step for exclusion forces for PME There are 4 inter charge-group virtual sites, will an extra communication step for selected coordinates and forces The initial number of communication pulses is: X 1 Y 1 The initial domain decomposition cell size is: X 2.25 nm Y 4.50 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 virtual site constructions (-rcon) 2.250 nm atoms separated by up to 5 constraints (-rcon) 2.250 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 Y 1 The minimum size for domain decomposition cells is 1.550 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.69 Y 0.34 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 virtual site constructions (-rcon) 1.550 nm atoms separated by up to 5 constraints (-rcon) 1.550 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 ++++ G. Bussi, D. Donadio and M. Parrinello Canonical sampling through velocity rescaling J. Chem. Phys. 126 (2007) pp. 014101 -------- -------- --- Thank You --- -------- -------- There are: 6207 Atoms There are: 4 VSites Charge group distribution at step 0: 406 379 520 522 385 382 335 284 Grid: 4 x 6 x 8 cells Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 1.44e-04 Initial temperature: 320.324 K Started mdrun on node 0 Thu Jan 1 01:00:00 1970 Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 2.02557e+02 1.10177e+03 7.79678e+00 1.97967e+00 -3.65830e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy -3.42249e+03 -3.02092e+03 -4.17123e+04 2.08030e+04 -2.09093e+04 Temperature Pressure (bar) Constr. rmsd 3.21017e+02 -3.86199e+02 1.35447e-04 DD step 4 load imb.: force 62.0% DD step 999 load imb.: force 24.0% Step Time Lambda 1000 20.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 3.32496e+03 7.12748e+03 2.21512e+01 9.42270e-01 -4.88496e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy -1.66849e+04 -1.12423e+04 -6.63012e+04 2.11618e+04 -4.51394e+04 Temperature Pressure (bar) Constr. rmsd 3.26555e+02 -6.09308e+01 1.88442e-04 DD step 1999 load imb.: force 26.8% Step Time Lambda 2000 40.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 3.48446e+03 6.88615e+03 4.14475e+01 1.86677e+00 -5.08523e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy -1.66986e+04 -1.13472e+04 -6.84842e+04 2.04649e+04 -4.80192e+04 Temperature Pressure (bar) Constr. rmsd 3.15801e+02 1.59258e+01 1.92954e-04 DD step 2999 load imb.: force 25.5% Step Time Lambda 3000 60.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 3.51178e+03 7.12330e+03 3.09578e+01 1.54288e+00 -5.18056e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy -1.72149e+04 -1.15563e+04 -6.99092e+04 2.11430e+04 -4.87662e+04 Temperature Pressure (bar) Constr. rmsd 3.26264e+02 2.24502e+01 2.01252e-04 DD step 3999 load imb.: force 25.7% Step Time Lambda 4000 80.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 3.34944e+03 6.74064e+03 1.02067e+01 3.92874e-01 -5.25131e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy -1.67403e+04 -1.15786e+04 -7.07314e+04 2.08154e+04 -4.99159e+04 Temperature Pressure (bar) Constr. rmsd 3.21209e+02 1.74034e+01 1.97665e-04 DD step 4999 load imb.: force 28.5% Step Time Lambda 5000 100.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 3.35397e+03 6.58430e+03 1.81552e+01 3.20741e-01 -5.26745e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy -1.67078e+04 -1.15452e+04 -7.09708e+04 2.03745e+04 -5.05963e+04 Temperature Pressure (bar) Constr. rmsd 3.14405e+02 -2.44230e+01 1.81251e-04 DD step 5999 load imb.: force 27.8% Step Time Lambda 6000 120.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 3.24776e+03 7.01385e+03 1.21300e+01 2.29243e+00 -5.34138e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy -1.73332e+04 -1.17036e+04 -7.21746e+04 2.13317e+04 -5.08429e+04 Temperature Pressure (bar) Constr. rmsd 3.29176e+02 9.76703e+00 2.12056e-04 DD step 6999 load imb.: force 30.4% Step Time Lambda 7000 140.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 3.35869e+03 6.80586e+03 2.33980e+01 1.49204e+00 -5.32661e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy -1.72877e+04 -1.16177e+04 -7.19822e+04 2.08391e+04 -5.11431e+04 Temperature Pressure (bar) Constr. rmsd 3.21574e+02 3.57865e+01 1.85294e-04 DD step 7999 load imb.: force 32.1% Step Time Lambda 8000 160.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 3.24736e+03 6.99970e+03 1.00338e+01 1.38263e+00 -5.35303e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy -1.75113e+04 -1.16710e+04 -7.24542e+04 2.03733e+04 -5.20809e+04 Temperature Pressure (bar) Constr. rmsd 3.14386e+02 -1.24529e+01 2.00285e-04 DD step 8999 load imb.: force 37.7% Step Time Lambda 9000 180.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 3.32796e+03 7.01965e+03 1.35132e+01 2.09261e+00 -5.37537e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy -1.76204e+04 -1.17734e+04 -7.27843e+04 2.06194e+04 -5.21648e+04 Temperature Pressure (bar) Constr. rmsd 3.18185e+02 -4.13071e+01 1.95674e-04 Received the INT signal, stopping at the next NS step Step Time Lambda 9795 195.90000 0.00000 Writing checkpoint, step 9795 at Thu Mar 10 16:11:38 2016 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 3.38839e+03 6.82873e+03 2.30292e+01 3.77311e-01 -5.45082e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy -1.75413e+04 -1.16630e+04 -7.34719e+04 2.10823e+04 -5.23897e+04 Temperature Pressure (bar) Constr. rmsd 3.25327e+02 5.19898e+01 0.00000e+00 <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 9796 steps using 99 frames Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 3.35448e+03 6.85907e+03 2.18744e+01 1.40014e+00 -5.15003e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy -1.67889e+04 -1.14127e+04 -6.94651e+04 2.08646e+04 -4.86005e+04 Temperature Pressure (bar) Constr. rmsd 3.21968e+02 2.58678e+00 0.00000e+00 Box-X Box-Y Box-Z 7.27176e+00 7.27176e+00 7.27176e+00 Total Virial (kJ/mol) 6.98591e+03 6.00027e+01 -1.04658e+02 6.00021e+01 6.96492e+03 -9.31689e+00 -1.04658e+02 -9.31600e+00 6.97330e+03 Pressure (bar) 2.97229e+00 -4.16166e+00 8.23864e+00 -4.16161e+00 2.25042e+00 1.18107e+00 8.23858e+00 1.18099e+00 2.53764e+00 Epot (kJ/mol) Coul-SR LJ-SR Protein-Protein -1.40608e+02 -3.40804e+02 Protein-POPC -8.77082e+00 -1.00106e+02 Protein-PW_NA+ -1.93236e+02 -5.75849e+02 POPC-POPC -8.11503e+02 -1.66486e+04 POPC-PW_NA+ -5.46433e+03 -1.42941e+04 PW_NA+-PW_NA+ -1.01705e+04 -1.95409e+04 T-Protein T-POPC T-PW_NA+ 3.14091e+02 3.22882e+02 3.21611e+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] 724.027334 724.027 0.0 NB VdW [F] 61054.224646 61054.225 3.5 NB Elec. [V&F] 1340.881160 1340.881 0.1 NB Elec. [F] 88324.429305 88324.429 5.1 NB VdW & Elec. [V&F] 24.419365 24.419 0.0 NB VdW & Elec. [F] 1668.940704 1668.941 0.1 Calc Weights 182.528868 6571.039 0.4 Spread Q Bspline 3893.949184 7787.898 0.4 Gather F Bspline 3893.949184 23363.695 1.3 3D-FFT 190247.743752 1521981.950 87.1 Solve PME 125.388800 8024.883 0.5 NS-Pairs 788.488813 16558.265 0.9 Reset In Box 6.297480 18.892 0.0 CG-CoM 12.179771 36.539 0.0 Bonds 15.183800 895.844 0.1 Angles 26.321852 4422.071 0.3 Propers 0.156736 35.893 0.0 Impropers 0.019592 4.075 0.0 Virial 12.879160 231.825 0.0 Stop-CM 0.614889 6.149 0.0 Calc-Ekin 24.347120 657.372 0.0 Lincs 29.848929 1790.936 0.1 Lincs-Mat 181.584504 726.338 0.0 Constraint-V 59.691780 477.534 0.0 Constraint-Vir 5.971027 143.305 0.0 Virtual Site 2 0.047024 1.082 0.0 ----------------------------------------------------------------------------- Total 1746872.508 100.0 ----------------------------------------------------------------------------- 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 7176.6 av. #atoms communicated per step for vsites: 3 x 0.7 av. #atoms communicated per step for LINCS: 2 x 19.9 Average load imbalance: 29.9 % Part of the total run time spent waiting due to load imbalance: 2.2 % 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 1960 0.859 17.137 1.8 DD comm. load 8 1 99 0.003 0.050 0.0 Vsite constr. 8 1 9796 0.025 0.506 0.1 Neighbor search 8 1 1960 2.459 49.062 5.1 Comm. coord. 8 1 9796 0.325 6.483 0.7 Force 8 1 9796 4.629 92.362 9.5 Wait + Comm. F 8 1 9796 0.142 2.842 0.3 PME mesh 8 1 9796 38.769 773.501 79.9 Vsite spread 8 1 11756 0.025 0.490 0.1 Write traj. 8 1 3 0.004 0.071 0.0 Update 8 1 9796 0.430 8.575 0.9 Constraints 8 1 9796 0.603 12.038 1.2 Comm. energies 8 1 1960 0.113 2.252 0.2 Rest 8 0.165 3.284 0.3 ----------------------------------------------------------------------------- Total 8 48.550 968.654 100.0 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- PME redist. X/F 8 1 19592 2.461 49.095 5.1 PME spread/gather 8 1 19592 3.040 60.658 6.3 PME 3D-FFT 8 1 19592 24.769 494.183 51.0 PME 3D-FFT Comm. 8 1 39184 5.347 106.685 11.0 PME solve 8 1 9796 3.137 62.580 6.5 ----------------------------------------------------------------------------- Core t (s) Wall t (s) (%) Time: 388.180 48.550 799.5 (ns/day) (hour/ns) Performance: 348.662 0.069 Finished mdrun on node 0 Thu Mar 10 16:11:38 2016