Log file opened: nodeid 0, nnodes = 1, host = winesap.local, process = 740 :-) G R O M A C S (-: GROtesk MACabre and Sinister :-) VERSION 3.2.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2004, 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. :-) mdrun_d (double precision) (-: ++++++++ PLEASE 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 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 --- -------- -------- There are 0 atoms for free energy perturbation Input Parameters: integrator = md nsteps = 5000 init_step = 0 ns_type = Grid nstlist = 10 ndelta = 2 bDomDecomp = FALSE decomp_dir = 0 nstcomm = 1 nstcheckpoint = 1000 nstlog = 0 nstxout = 0 nstvout = 0 nstfout = 0 nstenergy = 0 nstxtcout = 0 init_t = 0 delta_t = 0.002 xtcprec = 1000 nkx = 0 nky = 0 nkz = 0 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = FALSE ePBC = xyz bUncStart = FALSE bShakeSOR = FALSE etc = Berendsen epc = No epctype = Isotropic tau_p = 1 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} compress (3x3): compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} andersen_seed = 815131 rlist = 0.8 coulombtype = Cut-off rcoulomb_switch = 0 rcoulomb = 0.8 vdwtype = Cut-off rvdw_switch = 0 rvdw = 0.8 epsilon_r = 1 tabext = 1 gb_algorithm = Still nstgbradii = 1 rgbradii = 2 gb_saltconc = 0 implicit_solvent = No DispCorr = No fudgeQQ = 1 free_energy = no init_lambda = 0 sc_alpha = 0 sc_sigma = 0.3 delta_lambda = 0 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 dihre-tau = 0 nstdihreout = 100 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_temp = 300 bd_fric = 0 ld_seed = 1993 cos_accel = 0 userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 grpopts: nrdf: 1072.83 17997.2 ref_t: 300 300 tau_t: 0.1 0.1 anneal: No No ann_npoints: 0 0 acc: 0 0 0 nfreeze: N N N energygrp_excl[ 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 CPU= 0, lastcg= 3167, targetcg= 1584, myshift= 0 nsb->shift = 1, nsb->bshift= 0 Neighbor Search Blocks nsb->nodeid: 0 nsb->nnodes: 1 nsb->cgtotal: 3168 nsb->natoms: 9389 nsb->shift: 1 nsb->bshift: 0 Nodeid index homenr cgload workload 0 0 9389 3168 3168 Max number of graph edges per atom is 10 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 0.8 Coulomb: 0.8 LJ: 0.8 Generated table with 2000 data points for COUL. Tabscale = 2000 points/nm Generated table with 2000 data points for LJ6. Tabscale = 2000 points/nm Generated table with 2000 data points for LJ12. Tabscale = 2000 points/nm Going to determine what solvent types we have. There are 3001 molecules, 3168 charge groups and 9389 atoms There are 0 optimized solvent molecules on node 0 There are 3000 optimized water molecules on node 0 Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest, initial mass: 58238.1 There are: 9389 Atom Removing pbc first time Done rmpbc Constraining the starting coordinates (step -2) ++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++ H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 (1984) pp. 3684-3690 -------- -------- --- Thank You --- -------- -------- ++++++++ PLEASE 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 --- -------- -------- ++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++ B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije LINCS: A Linear Constraint Solver for molecular simulations J. Comp. Chem. 18 (1997) pp. 1463-1472 -------- -------- --- Thank You --- -------- -------- Initializing LINear Constraint Solver number of constraints is 94 average number of constraints coupled to one constraint is 0.5 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.010152 87 88 0.004417 After LINCS 0.000000 201 203 0.000000 Going to use C-settle (3000 waters) wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.081665, ra = 0.00645837 rb = 0.051255, rc2 = 0.16333, rone = 1, dHH = 0.16333, dOH = 0.1 Constraining the coordinates at t0-dt (step -1) Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.000482 195 196 0.000165 After LINCS 0.000024 1 2 0.000004 Started mdrun on node 0 Tue Jun 7 11:44:10 2005 Initial temperature: 308.341 K Grid: 12 x 11 x 10 cells Step Time Lambda 5000 10.00000 0.00000 Energies (kJ/mol) G96Bond G96Angle Proper Dih. Improper Dih. LJ-14 3.83039e+02 6.52744e+02 3.69092e+02 2.22784e+02 1.49429e+02 Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En. 4.01678e+03 1.99687e+04 -1.54984e+05 -1.29222e+05 2.41005e+04 Total Energy Temperature Pressure (bar) -1.05121e+05 3.03997e+02 -2.01234e+02 <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Energies (kJ/mol) G96Bond G96Angle Proper Dih. Improper Dih. LJ-14 3.76161e+02 6.73115e+02 3.03842e+02 2.06619e+02 1.89760e+02 Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En. 3.97061e+03 2.02765e+04 -1.55428e+05 -1.29431e+05 2.41769e+04 Total Energy Temperature Pressure (bar) -1.05254e+05 3.04960e+02 2.41423e+01 Total Virial (kJ/mol) 8.03222e+03 4.02975e+01 -7.54397e-01 4.02975e+01 8.01745e+03 1.84039e+01 -7.54397e-01 1.84039e+01 7.91397e+03 Pressure (bar) 1.32816e+01 -2.19282e+01 7.82983e+00 -2.19282e+01 1.05143e+01 -8.90704e+00 7.82983e+00 -8.90704e+00 4.86309e+01 Total Dipole (Debye) 2.19450e+02 2.14556e+02 2.22054e+02 T-Protein T-SOL 3.04862e+02 3.04966e+02 <====== ############################### ==> <==== R M S - F L U C T U A T I O N S ====> <== ############################### ======> Energies (kJ/mol) G96Bond G96Angle Proper Dih. Improper Dih. LJ-14 2.93092e+01 3.70268e+01 2.35555e+01 1.99704e+01 2.15765e+01 Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En. 3.09448e+01 3.87381e+02 5.86953e+02 3.92677e+02 1.78109e+02 Total Energy Temperature Pressure (bar) 3.50384e+02 2.24661e+00 2.57566e+02 Total Virial (kJ/mol) 1.11771e+03 6.41387e+02 6.75061e+02 6.41387e+02 1.00898e+03 6.65207e+02 6.75061e+02 6.65207e+02 1.10987e+03 Pressure (bar) 3.80591e+02 2.20000e+02 2.31457e+02 2.20000e+02 3.43258e+02 2.28455e+02 2.31457e+02 2.28455e+02 3.77481e+02 Total Dipole (Debye) 2.84818e+01 2.68316e+01 2.75848e+01 T-Protein T-SOL 1.01618e+01 2.26672e+00 M E G A - F L O P S A C C O U N T I N G RF=Reaction-field Free=Free Energy SC=Softcore T=Tabulated S=Solvent W=Water WW=Water-Water Computing: M-Number M-Flop's % Flop's LJ 48.643196 1507.939076 1.0 Coulomb 64.462147 1740.477969 1.2 Coulomb(W) 4.019642 325.591002 0.2 LJ + Coulomb 56.585456 2150.247328 1.4 LJ + Coul(W) 16.280854 1497.838568 1.0 LJ + Coul(WW) 500.894140 122719.064300 82.6 Innerloop-Iatom 291.133885 2911.338850 2.0 NS-Pairs 144.926992 3043.466832 2.0 Reset In Box 4.703889 42.335001 0.0 Shift-X 187.817556 1126.905336 0.8 CG-CoM 1.587168 46.027872 0.0 Bonds 1.505301 64.727943 0.0 Angles 2.900580 472.794540 0.3 Propers 1.000200 229.045800 0.2 Impropers 0.980196 203.880768 0.1 Virial 47.089416 847.609488 0.6 Update 46.954389 1455.586059 1.0 Stop-CM 46.945000 469.450000 0.3 Calc-Ekin 46.963778 1268.022006 0.9 Lincs 0.470282 28.216920 0.0 Lincs-Mat 1.440864 5.763456 0.0 Shake-V 46.954389 704.315835 0.5 Shake-Vir 46.954389 845.179002 0.6 Settle 15.009000 4847.907000 3.3 Total 148553.73095 100.0 NODE (s) Real (s) (%) Time: 701.240 715.000 98.1 11:41 (Mnbf/s) (MFlops) (ps/NODE hour) (NODE hour/ns) Performance: 6.758 211.844 51.338 19.479 Finished mdrun on node 0 Tue Jun 7 11:56:05 2005