Log file opened on Mon May 10 22:43:13 2010 Host: linux2cpu pid: 19390 nodeid: 0 nnodes: 2 The Gromacs distribution was built Wed Apr 28 21:57:46 PDT 2010 by leontyev@linux2cpu (Linux 2.6.31-14-generic i686) :-) G R O M A C S (-: Grunge ROck MAChoS :-) VERSION 4.0.7 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, 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 General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /home/leontyev/programs/bin/gromacs/gromacs-4.0.7/bin/mdrun_mpi (-: ++++ 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 --- -------- -------- parameters of the run: integrator = md nsteps = 3 init_step = 0 ns_type = Grid nstlist = 1 ndelta = 2 nstcomm = 1003 comm_mode = Linear nstlog = 1 nstxout = 1 nstvout = 1000000 nstfout = 0 nstenergy = 0 nstxtcout = 100 init_t = 0 delta_t = 0.001 xtcprec = 1000 nkx = 16 nky = 16 nkz = 16 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = TRUE ePBC = xyz bPeriodicMols = FALSE bContinuation = FALSE bShakeSOR = FALSE etc = V-rescale epc = Berendsen epctype = Isotropic tau_p = 0.5 ref_p (3x3): ref_p[ 0]={ 1.01325e+00, 0.00000e+00, 0.00000e+00} ref_p[ 1]={ 0.00000e+00, 1.01325e+00, 0.00000e+00} ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.01325e+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 andersen_seed = 815131 rlist = 0.9 rtpi = 0.05 coulombtype = PME rcoulomb_switch = 0 rcoulomb = 0.9 vdwtype = Switch rvdw_switch = 0.8 rvdw = 0.9 epsilon_r = 1 epsilon_rf = 1 tabext = 1 implicit_solvent = No gb_algorithm = Still gb_epsilon_solvent = 80 nstgbradii = 1 rgbradii = 2 gb_saltconc = 0 gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 sa_surface_tension = 2.092 DispCorr = No free_energy = no init_lambda = 0 sc_alpha = 0 sc_power = 0 sc_sigma = 0.3 delta_lambda = 0 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 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 = 1000 em_stepsize = 0.01 em_tol = 10 niter = 20 fc_stepsize = 0 nstcgsteep = 1000 nbfgscorr = 10 ConstAlg = Lincs shake_tol = 0.0001 lincs_order = 8 lincs_warnangle = 30 lincs_iter = 4 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} userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 grpopts: nrdf: 1293 ref_t: 298.15 tau_t: 0.4 anneal: No ann_npoints: 0 acc: 0 0 0 nfreeze: N N N energygrp_flags[ 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 2 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Using 0 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 2 cells with a minimum initial size of 0.000 nm Domain decomposition grid 2 x 1 x 1, separate PME nodes 0 Domain decomposition nodeid 0, coordinates 0 0 0 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. Essman, L. Perela, 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 --- -------- -------- Using a Gaussian width (1/beta) of 0.288146 nm for Ewald Using shifted Lennard-Jones, switch between 0.8 and 0.9 nm Cut-off's: NS: 0.9 Coulomb: 0.9 LJ: 0.9 System total charge: 0.000 Generated table with 949 data points for Ewald. Tabscale = 500 points/nm Generated table with 949 data points for LJ6Switch. Tabscale = 500 points/nm Generated table with 949 data points for LJ12Switch. Tabscale = 500 points/nm Enabling SPC water optimization for 216 molecules. Configuring nonbonded kernels... Testing AMD 3DNow support... present. Testing ia32 SSE support... present. Removing pbc first time ++++ 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 The initial number of communication pulses is: X 1 The initial domain decomposition cell size is: X 0.93 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 0.900 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.97 Making 1D domain decomposition grid 2 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: 648 Atoms Charge group distribution at step 0: 112 104 Grid: 4 x 3 x 3 cells Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 0.00e+00 Initial temperature: 295.174 K Started mdrun on node 0 Mon May 10 22:43:13 2010 Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.73768e+03 -1.04948e+04 -1.13345e+03 -9.89062e+03 1.58418e+03 Total Energy Temperature Pressure (bar) -8.30643e+03 2.94714e+02 -9.93848e+02 DD step 0 load imb.: force 3.4% Step Time Lambda 1 0.00100 0.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.74016e+03 -1.04980e+04 -1.13343e+03 -9.89129e+03 1.58076e+03 Total Energy Temperature Pressure (bar) -8.31053e+03 2.94077e+02 -1.00574e+03 DD step 1 load imb.: force 4.8% Step Time Lambda 2 0.00200 0.00000 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.74386e+03 -1.05013e+04 -1.13355e+03 -9.89099e+03 1.57833e+03 Total Energy Temperature Pressure (bar) -8.31266e+03 2.93625e+02 -8.76862e+02 DD step 2 load imb.: force 4.7% Step Time Lambda 3 0.00300 0.00000 Writing checkpoint, step 3 at Mon May 10 22:43:13 2010 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.74753e+03 -1.05050e+04 -1.13392e+03 -9.89135e+03 1.57988e+03 Total Energy Temperature Pressure (bar) -8.31147e+03 2.93914e+02 -1.04271e+03 <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 1.74231e+03 -1.04998e+04 -1.13359e+03 -9.89106e+03 1.58079e+03 Total Energy Temperature Pressure (bar) -8.31027e+03 2.94082e+02 -9.79791e+02 Box-X Box-Y Box-Z Volume Density (SI) 1.86213e+00 1.86213e+00 1.86213e+00 6.45697e+00 1.00073e+03 pV -3.80989e+02 Total Virial (kJ/mol) 5.29053e+02 -1.43883e+02 3.19513e+01 -1.42722e+02 7.30120e+02 3.61000e+02 3.40775e+01 3.62024e+02 8.93101e+02 Pressure (bar) -1.30920e+02 6.44623e+02 -2.38167e+02 6.38654e+02 -9.86450e+02 -1.97823e+03 -2.49101e+02 -1.98350e+03 -1.82200e+03 Total Dipole (Debye) -6.42935e+00 -4.94569e+01 2.05969e+01 <====== ############################### ==> <==== R M S - F L U C T U A T I O N S ====> <== ############################### ======> Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 3.73203e+00 3.76128e+00 1.98687e-01 2.90071e-01 2.14454e+00 Total Energy Temperature Pressure (bar) 2.34227e+00 3.98954e-01 6.20974e+01 Box-X Box-Y Box-Z Volume Density (SI) 4.63307e-05 4.63307e-05 4.63307e-05 4.81890e-04 7.47020e-02 pV 2.41422e+01 Total Virial (kJ/mol) 1.46562e+01 1.01271e+00 1.19238e+01 4.24951e+00 1.33076e+01 3.08082e+00 9.20050e+00 4.58247e+00 1.40094e+01 Pressure (bar) 6.97367e+01 6.75782e+00 4.46411e+01 2.81607e+01 6.66501e+01 3.42068e+01 3.12562e+01 4.14704e+01 6.76055e+01 Total Dipole (Debye) 1.07159e+00 7.13585e-01 6.59717e-01 M E G A - F L O P S A C C O U N T I N G RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs) NF=No Forces Computing: M-Number M-Flops % Flops ----------------------------------------------------------------------- Coul(T) + VdW(T) [W3-W3] 0.043554 17.204 62.9 Outer nonbonded loop 0.023744 0.237 0.9 Calc Weights 0.007776 0.280 1.0 Spread Q Bspline 0.165888 0.332 1.2 Gather F Bspline 0.165888 1.991 7.3 3D-FFT 0.393200 3.146 11.5 Solve PME 0.009216 0.590 2.2 NS-Pairs 0.133445 2.802 10.2 Reset In Box 0.000864 0.003 0.0 CG-CoM 0.003240 0.010 0.0 Virial 0.002952 0.053 0.2 Update 0.002592 0.080 0.3 Stop-CM 0.000648 0.006 0.0 P-Coupling 0.002592 0.016 0.1 Calc-Ekin 0.003240 0.087 0.3 Constraint-V 0.003240 0.026 0.1 Constraint-Vir 0.002592 0.062 0.2 Settle 0.001296 0.419 1.5 ----------------------------------------------------------------------- Total 27.343 100.0 ----------------------------------------------------------------------- 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 624.6 Average load imbalance: 4.3 % Part of the total run time spent waiting due to load imbalance: 1.2 % 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 Number G-Cycles Seconds % ----------------------------------------------------------------------- Domain decomp. 2 4 0.005 0.0 5.6 Comm. coord. 2 4 0.001 0.0 0.7 Neighbor search 2 4 0.014 0.0 14.7 Force 2 4 0.021 0.0 21.6 Wait + Comm. F 2 4 0.001 0.0 0.7 PME mesh 2 4 0.017 0.0 18.0 Write traj. 2 4 0.016 0.0 16.7 Update 2 4 0.001 0.0 1.0 Constraints 2 4 0.001 0.0 1.1 Comm. energies 2 4 0.016 0.0 16.8 Rest 2 0.003 0.0 3.1 ----------------------------------------------------------------------- Total 2 0.097 0.0 100.0 ----------------------------------------------------------------------- NOTE: 17 % of the run time was spent communicating energies, you might want to use the -nosum option of mdrun Parallel run - timing based on wallclock. Finished mdrun on node 0 Mon May 10 22:43:13 2010