Log file opened on Wed Apr 6 12:13:57 2016 Host: node11 pid: 15179 rank ID: 0 number of ranks: 1 GROMACS: gmx mdrun, VERSION 5.0 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Peter Kasson Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2014, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS 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. GROMACS: gmx mdrun, VERSION 5.0 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: gmx mdrun -nt 8 -c confout.pdb -v -deffnm em-const Gromacs version: VERSION 5.0 Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled GPU support: disabled invsqrt routine: gmx_software_invsqrt(x) SIMD instructions: SSE4.1 FFT library: fftw-3.3.3-sse2 RDTSCP usage: disabled C++11 compilation: enabled TNG support: enabled Tracing support: disabled Built on: Thu Oct 30 09:03:21 PKT 2014 Built by: root@mcg09 [CMAKE] Build OS/arch: Linux 3.11.10-21-desktop x86_64 Build CPU vendor: GenuineIntel Build CPU brand: Intel(R) Xeon(R) CPU E5405 @ 2.00GHz Build CPU family: 6 Model: 23 Stepping: 6 Build CPU features: apic clfsh cmov cx8 cx16 lahf_lm mmx msr pdcm pse sse2 sse3 sse4.1 ssse3 C compiler: /usr/bin/cc GNU 4.8.1 C compiler flags: -msse4.1 -Wno-maybe-uninitialized -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU 4.8.1 C++ compiler flags: -msse4.1 -std=c++0x -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds -O3 -DNDEBUG Boost version: 1.53.0 (external) ++++ 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 tinit = 0 dt = 0.001 nsteps = 1000 init-step = 0 simulation-part = 1 comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = 3608644490 emtol = 1000 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstcalcenergy = 100 nstenergy = 1000 nstxout-compressed = 0 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 1 ns-type = Grid pbc = xyz periodic-molecules = FALSE verlet-buffer-tolerance = 0.005 rlist = 1 rlistlong = 1 nstcalclr = 1 coulombtype = Cut-off coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 1 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = Potential-shift rvdw-switch = 0 rvdw = 1 DispCorr = No table-extension = 1 fourierspacing = 0.16 fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 pme-order = 4 ewald-rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 0 epsilon-surface = 0 implicit-solvent = GBSA gb-algorithm = Still nstgbradii = 1 rgbradii = 1 gb-epsilon-solvent = 80 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 = 0.0054 tcoupl = No nsttcouple = -1 nh-chain-length = 0 print-nose-hoover-chain-variables = FALSE pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 compressibility (3x3): compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 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} 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 QMMM = FALSE QMconstraints = 0 QMMMscheme = 0 MMChargeScaleFactor = 1 qm-opts: ngQM = 0 constraint-algorithm = Lincs continuation = FALSE Shake-SOR = FALSE shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 nwall = 0 wall-type = 9-3 wall-r-linpot = -1 wall-atomtype[0] = -1 wall-atomtype[1] = -1 wall-density[0] = 0 wall-density[1] = 0 wall-ewald-zfac = 3 pull = no rotation = FALSE interactiveMD = FALSE disre = Simple disre-weighting = Conservative disre-mixed = FALSE dr-fc = 1000 dr-tau = 0 nstdisreout = 100 orire-fc = 0 orire-tau = 0 nstorireout = 100 free-energy = no cos-acceleration = 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} simulated-tempering = FALSE E-x: n = 0 E-xt: n = 0 E-y: n = 0 E-yt: n = 0 E-z: n = 0 E-zt: n = 0 swapcoords = no adress = FALSE userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 grpopts: nrdf: 15156.5 ref-t: 0 tau-t: 0 annealing: No annealing-npoints: 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 Using 1 MPI thread Using 8 OpenMP threads Detecting CPU SIMD instructions. Present hardware specification: Vendor: GenuineIntel Brand: Intel(R) Xeon(R) CPU E7- 2820 @ 2.00GHz Family: 6 Model: 47 Stepping: 2 Features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 x2apic SIMD instructions most likely to fit this hardware: SSE4.1 SIMD instructions selected at GROMACS compile time: SSE4.1 The current CPU can measure timings more accurately than the code in gmx was configured to use. This might affect your simulation speed as accurate timings are needed for load-balancing. Please consider rebuilding gmx with the GMX_USE_RDTSCP=OFF CMake option. Cut-off's: NS: 1 Coulomb: 1 LJ: 1 System total charge: -11.000 Generated table with 1000 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1000 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1000 data points for 1-4 LJ12. Tabscale = 500 points/nm Using SSE4.1 4x4 non-bonded kernels Using geometric Lennard-Jones combination rule Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Coulomb -1e+00 Removing pbc first time NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin thread to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). 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 42 42 constraints are involved in constraint triangles, will apply an additional matrix expansion of order 4 for couplings between constraints inside triangles Initiating Steepest Descents Rel. Constraint Deviation: RMS MAX between atoms Before LINCS 0.002812 0.008943 1072 1073 After LINCS 47.479051 104.334671 1062 1068 Step -1, time -0.001 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 47.479051, max 104.334671 (between atoms 1062 and 1068) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Constraint error in algorithm Lincs at step -1 Wrote pdb files with previous and current coordinates Started Steepest Descents on rank 0 Wed Apr 6 12:13:57 2016 Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 1000 Step Time Lambda 0 0.00000 0.00000 Step Time Lambda 1 1.00000 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell.GB Polarization 7.26459e+07 8.52412e+03 1.20697e+02 3.85646e+03 -1.07086e+05 Nonpolar Sol. LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) 1.24882e+01 9.40966e+03 3.15420e+04 5.17337e+03 -8.43225e+04 Potential Pressure (bar) 7.25131e+07 5.11945e+05 Step Time Lambda 2 2.00000 0.00000 Step Time Lambda 3 3.00000 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell.GB Polarization 6.57094e+07 9.30564e+03 8.99437e+01 3.91153e+03 -1.07093e+05 Nonpolar Sol. LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) 1.24882e+01 9.40966e+03 3.15415e+04 1.53175e+05 -8.43347e+04 Potential Pressure (bar) 6.57254e+07 -1.18320e+05 Step Time Lambda 4 4.00000 0.00000 Step Time Lambda 5 5.00000 0.00000 Step Time Lambda 6 6.00000 0.00000 Step Time Lambda 7 7.00000 0.00000 Step Time Lambda 8 8.00000 0.00000 Step Time Lambda 9 9.00000 0.00000 Step Time Lambda 10 10.00000 0.00000 Step Time Lambda 11 11.00000 0.00000 Step Time Lambda 12 12.00000 0.00000 Step Time Lambda 13 13.00000 0.00000 Step Time Lambda 14 14.00000 0.00000 Step Time Lambda 15 15.00000 0.00000 Step Time Lambda 16 16.00000 0.00000 Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) Steepest Descents converged to machine precision in 17 steps, but did not reach the requested Fmax < 1000. Potential Energy = 6.5725412e+07 Maximum force = 6.5482104e+07 on atom 1062 Norm of force = 1.5786262e+06 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 ----------------------------------------------------------------------------- Pair Search distance check 10.897212 98.075 5.3 NxN RF Elec. + LJ [V&F] 29.901360 1614.673 87.2 NxN RF Electrostatics [V&F] 1.008528 36.307 2.0 1,4 nonbonded interactions 0.226627 20.396 1.1 Shift-X 0.086139 0.517 0.0 Bonds 0.087278 5.149 0.3 Angles 0.157046 26.384 1.4 Propers 0.018377 4.208 0.2 RB-Dihedrals 0.176919 43.699 2.4 Virial 0.086904 1.564 0.1 Lincs 0.001428 0.086 0.0 Lincs-Mat 0.125256 0.501 0.0 Constraint-Vir 0.000714 0.017 0.0 ----------------------------------------------------------------------------- Total 1851.577 100.0 ----------------------------------------------------------------------------- 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 On 1 MPI rank, each using 8 OpenMP threads Computing: Num Num Call Wall time Giga-Cycles Ranks Threads Count (s) total sum % ----------------------------------------------------------------------------- Neighbor search 1 8 17 0.019 0.597 1.3 Force 1 8 17 0.076 2.431 5.2 NB X/F buffer ops. 1 8 17 0.000 0.011 0.0 Constraints 1 8 33 0.594 18.971 40.8 Rest 0.766 24.449 52.6 ----------------------------------------------------------------------------- Total 1.455 46.459 100.0 ----------------------------------------------------------------------------- Core t (s) Wall t (s) (%) Time: 10.231 1.455 703.0 (steps/hour) Performance: 42048.1 Finished mdrun on rank 0 Wed Apr 6 12:13:58 2016