Log file opened on Fri Nov 21 15:18:32 2014 Host: Labtop.local pid: 24569 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 (-: Gallium Rubidium Oxygen Manganese Argon Carbon Silicon :-) 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 = 2500000 init-step = 0 cutoff-scheme = Group ns_type = Grid nstlist = 5 ndelta = 2 nstcomm = 100 comm-mode = Linear nstlog = 500 nstxout = 0 nstvout = 0 nstfout = 0 nstcalcenergy = 100 nstenergy = 500 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: 107.979 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 4 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: 0.570 nm, Bond, atoms 36 37 multi-body bonded interactions: 1.001 nm, G96Angle, atoms 949 951 Minimum cell size due to bonded interactions: 1.101 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 1.570 nm Estimated maximum distance required for P-LINCS: 1.570 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 4 cells with a minimum initial size of 1.963 nm The maximum allowed number of cells is: X 4 Y 4 Z 4 Domain decomposition grid 4 x 1 x 1, separate PME nodes 0 PME domain decomposition: 4 x 1 x 1 Domain decomposition nodeid 0, coordinates 0 0 0 Using 4 MPI threads 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: 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 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 3034 There are inter charge-group constraints, will communicate selected coordinates each lincs iteration 12 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 1589 inter charge-group exclusions, will use an extra communication step for exclusion forces for PME The initial number of communication pulses is: X 1 The initial domain decomposition cell size is: X 2.25 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) 2.250 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 The minimum size for domain decomposition cells is 1.570 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 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) 1.200 nm atoms separated by up to 5 constraints (-rcon) 1.570 nm Making 1D domain decomposition grid 4 x 1 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: 6210 Atoms Charge group distribution at step 0: 746 1061 783 622 Grid: 4 x 8 x 8 cells Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 1.34e-04 Initial temperature: 320.851 K Started mdrun on node 0 Fri Nov 21 15:18:32 2014 Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 2.00122e+02 1.12077e+03 6.92905e+00 1.55064e+00 -3.72164e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy -3.28932e+03 -3.02030e+03 -4.21966e+04 2.08396e+04 -2.13571e+04 Temperature Pressure (bar) Constr. rmsd 3.21479e+02 -3.83767e+02 1.41411e-04 DD step 4 load imb.: force 60.8% DD step 499 load imb.: force 38.9% Step Time Lambda 500 10.00000 0.00000 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 3.29864e+03 6.90829e+03 2.17077e+01 2.82956e+00 -4.33802e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy -1.50218e+04 -1.06865e+04 -5.88571e+04 2.14050e+04 -3.74521e+04 Temperature Pressure (bar) Constr. rmsd 3.30201e+02 -4.69154e+01 2.10189e-04 Received the INT signal, stopping at the next NS step Step Time Lambda 550 11.00000 0.00000 Writing checkpoint, step 550 at Fri Nov 21 15:18:37 2014 Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 3.33875e+03 6.94279e+03 2.00149e+01 1.83981e+00 -4.42571e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy -1.51335e+04 -1.07826e+04 -5.98699e+04 2.16974e+04 -3.81724e+04 Temperature Pressure (bar) Constr. rmsd 3.34712e+02 1.63423e+01 0.00000e+00 <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 551 steps using 7 frames Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 2.67207e+03 5.85082e+03 1.64536e+01 2.94694e+00 -3.93202e+04 Coulomb (SR) Coul. recip. Potential Kinetic En. Total Energy -1.19564e+04 -8.89670e+03 -5.16310e+04 2.18974e+04 -2.97336e+04 Temperature Pressure (bar) Constr. rmsd 3.37797e+02 -7.25652e+01 0.00000e+00 Box-X Box-Y Box-Z 8.45082e+00 8.45082e+00 8.45082e+00 Total Virial (kJ/mol) 8.80200e+03 -1.53831e+01 -2.89126e+02 -1.53823e+01 8.68046e+03 -2.35156e+01 -2.89125e+02 -2.35160e+01 9.09858e+03 Pressure (bar) -7.08447e+01 3.00960e-01 1.72400e+01 3.00928e-01 -5.98537e+01 -3.93273e-02 1.72399e+01 -3.93040e-02 -8.69971e+01 Epot (kJ/mol) Coul-SR LJ-SR Protein-Protein 2.27546e-01 -4.84559e+02 Protein-POPC -4.35134e+01 -3.00542e+02 Protein-PW_CL- -1.93196e+02 -4.54800e+02 POPC-POPC -6.73406e+02 -1.17701e+04 POPC-PW_CL- -3.65135e+03 -1.14219e+04 PW_CL--PW_CL- -7.39516e+03 -1.48883e+04 T-Protein T-POPC T-PW_CL- 3.49565e+02 3.31920e+02 3.40472e+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] 40.725852 40.726 0.0 NB VdW [F] 2690.938544 2690.939 2.8 NB Elec. [V&F] 68.377632 68.378 0.1 NB Elec. [F] 3522.969968 3522.970 3.7 NB VdW & Elec. [V&F] 1.321429 1.321 0.0 NB VdW & Elec. [F] 71.138798 71.139 0.1 Calc Weights 10.265130 369.545 0.4 Spread Q Bspline 218.989440 437.979 0.5 Gather F Bspline 218.989440 1313.937 1.4 3D-FFT 10700.950062 85607.600 89.5 Solve PME 3.526400 225.690 0.2 NS-Pairs 34.656153 727.779 0.8 Reset In Box 0.356532 1.070 0.0 CG-CoM 0.695520 2.087 0.0 Bonds 0.854601 50.421 0.1 Angles 1.484394 249.378 0.3 Propers 0.007714 1.767 0.0 Impropers 0.002204 0.458 0.0 Virial 0.709290 12.767 0.0 Stop-CM 0.043470 0.435 0.0 Calc-Ekin 1.378620 37.223 0.0 Lincs 1.684218 101.053 0.1 Lincs-Mat 10.318944 41.276 0.0 Constraint-V 3.362346 26.899 0.0 Constraint-Vir 0.338064 8.114 0.0 ----------------------------------------------------------------------------- Total 95610.948 100.0 ----------------------------------------------------------------------------- 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 3341.1 av. #atoms communicated per step for LINCS: 2 x 12.6 Average load imbalance: 46.5 % Part of the total run time spent waiting due to load imbalance: 2.4 % 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. 4 1 111 0.065 0.677 1.4 DD comm. load 4 1 7 0.000 0.003 0.0 Neighbor search 4 1 111 0.208 2.156 4.4 Comm. coord. 4 1 551 0.027 0.281 0.6 Force 4 1 551 0.342 3.551 7.2 Wait + Comm. F 4 1 551 0.008 0.086 0.2 PME mesh 4 1 551 3.962 41.112 83.6 Write traj. 4 1 2 0.002 0.016 0.0 Update 4 1 551 0.043 0.442 0.9 Constraints 4 1 551 0.058 0.600 1.2 Comm. energies 4 1 111 0.013 0.132 0.3 Rest 4 0.014 0.140 0.3 ----------------------------------------------------------------------------- Total 4 4.741 49.196 100.0 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- PME redist. X/F 4 1 1102 0.312 3.241 6.6 PME spread/gather 4 1 1102 0.560 5.808 11.8 PME 3D-FFT 4 1 1102 2.205 22.882 46.5 PME 3D-FFT Comm. 4 1 1102 0.426 4.420 9.0 PME solve 4 1 551 0.458 4.750 9.7 ----------------------------------------------------------------------------- Core t (s) Wall t (s) (%) Time: 18.820 4.741 396.9 (ns/day) (hour/ns) Performance: 200.821 0.120 Finished mdrun on node 0 Fri Nov 21 15:18:37 2014