md.log

Log file opened on Fri Apr 24 17:59:09 2009
Host: imogen.local  pid: 26596  nodeid: 0  nnodes:  1
The Gromacs distribution was built Sat Apr 18 02:25:11 CEST 2009 by
sgr@imogen.local (Darwin 8.11.1 i386)


                         :-)  G  R  O  M  A  C  S  (-:

                God Rules Over Mankind, Animals, Cosmos and Such

                            :-)  VERSION 4.0.3  (-:


      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.

                                :-)  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           = steep
   nsteps               = 10000
   init_step            = 0
   ns_type              = Grid
   nstlist              = 10
   ndelta               = 2
   nstcomm              = 1
   comm_mode            = Linear
   nstlog               = 100
   nstxout              = 100
   nstvout              = 100
   nstfout              = 0
   nstenergy            = 100
   nstxtcout            = 0
   init_t               = 0
   delta_t              = 0.002
   xtcprec              = 1000
   nkx                  = 27
   nky                  = 27
   nkz                  = 27
   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                  = No
   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}
   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                = 1.3
   rtpi                 = 0.05
   coulombtype          = PME
   rcoulomb_switch      = 0
   rcoulomb             = 1.3
   vdwtype              = Cut-off
   rvdw_switch          = 0
   rvdw                 = 1.3
   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            = 1e-06
   lincs_order          = 4
   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:        6111
   ref_t:           0
   tau_t:           0
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
Table routines are used for coulomb: TRUE
Table routines are used for vdw:     FALSE
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 0.416211 nm for Ewald
Cut-off's:   NS: 1.3   Coulomb: 1.3   LJ: 1.3
System total charge: 0.000
Generated table with 1150 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1150 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1150 data points for LJ12.
Tabscale = 500 points/nm

Enabling SPC water optimization for 1019 molecules.

Configuring nonbonded kernels...
Testing AMD 3DNow support... not 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 --- -------- --------

Initiating Steepest Descents
Max number of connections per atom is 2
Total number of connections is 4076
Max number of graph edges per atom is 2
Total number of graph edges is 4076
Going to use C-settle (1019 waters)
wo = 0.333333, wh =0.333333, wohh = 3, rc = 0.08165, ra = 0.0384897
rb = 0.0192449, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
Started Steepest Descents on node 0 Fri Apr 24 17:59:10 2009
Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+01
   Number of steps    =        10000
Grid: 5 x 5 x 5 cells
           Step           Time         Lambda
              0        0.00000        0.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    7.19583e+03   -4.79754e+04   -1.61202e+03   -4.23916e+04   -1.42583e+03

           Step           Time         Lambda
              1        1.00000        0.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    6.66084e+03   -4.88555e+04   -1.63774e+03   -4.38324e+04   -3.32443e+03

           Step           Time         Lambda
              2        2.00000        0.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    6.20743e+03   -5.01711e+04   -1.65814e+03   -4.56218e+04   -5.33913e+03

           Step           Time         Lambda
              3        3.00000        0.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    6.04517e+03   -5.13423e+04   -1.66326e+03   -4.69604e+04   -6.57077e+03

           Step           Time         Lambda
              4        4.00000        0.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    6.15354e+03   -5.21078e+04   -1.64174e+03   -4.75960e+04   -6.86239e+03

           Step           Time         Lambda
              5        5.00000        0.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    6.05463e+03   -5.24763e+04   -1.66753e+03   -4.80892e+04   -7.37504e+03

           Step           Time         Lambda
              6        6.00000        0.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    6.22297e+03   -5.28842e+04   -1.65074e+03   -4.83120e+04   -7.25585e+03

           Step           Time         Lambda
              7        7.00000        0.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    6.17463e+03   -5.30731e+04   -1.66961e+03   -4.85681e+04   -7.51972e+03

           Step           Time         Lambda
              8        8.00000        0.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    6.41287e+03   -5.34355e+04   -1.64700e+03   -4.86697e+04   -7.19108e+03

           Step           Time         Lambda
              9        9.00000        0.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    6.32987e+03   -5.36170e+04   -1.66823e+03   -4.89553e+04   -7.53977e+03

           Step           Time         Lambda
             10       10.00000        0.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    6.87853e+03   -5.43738e+04   -1.64971e+03   -4.91450e+04   -6.76493e+03

           Step           Time         Lambda
             11       11.00000        0.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    6.83974e+03   -5.44541e+04   -1.66271e+03   -4.92771e+04   -6.86197e+03

           Step           Time         Lambda
             12       12.00000        0.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    6.81955e+03   -5.47153e+04   -1.66803e+03   -4.95638e+04   -7.16985e+03

           Step           Time         Lambda
             13       13.00000        0.00000

           Step           Time         Lambda
             14       14.00000        0.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    6.82090e+03   -5.47961e+04   -1.66703e+03   -4.96422e+04   -7.21646e+03

           Step           Time         Lambda
             15       15.00000        0.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    6.90244e+03   -5.50176e+04   -1.68666e+03   -4.98018e+04   -8.10071e+05

           Step           Time         Lambda
             16       16.00000        0.00000

           Step           Time         Lambda
             17       17.00000        0.00000

           Step           Time         Lambda
             18       18.00000        0.00000

           Step           Time         Lambda
             19       19.00000        0.00000

           Step           Time         Lambda
             20       20.00000        0.00000

           Step           Time         Lambda
             21       21.00000        0.00000

           Step           Time         Lambda
             22       22.00000        0.00000

           Step           Time         Lambda
             23       23.00000        0.00000

           Step           Time         Lambda
             24       24.00000        0.00000

           Step           Time         Lambda
             25       25.00000        0.00000

           Step           Time         Lambda
             26       26.00000        0.00000

           Step           Time         Lambda
             27       27.00000        0.00000

           Step           Time         Lambda
             28       28.00000        0.00000

           Step           Time         Lambda
             29       29.00000        0.00000

           Step           Time         Lambda
             30       30.00000        0.00000

           Step           Time         Lambda
             31       31.00000        0.00000


Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

Steepest Descents converged to machine precision in 32 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -4.9801805e+04
Maximum force     =  2.6740678e+06 on atom 2326
Norm of force     =  6.5699125e+04

	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) + LJ [W3-W3]               4.872595        1861.331    77.1
 Outer nonbonded loop               1.317095          13.171     0.5
 Calc Weights                       0.293472          10.565     0.4
 Spread Q Bspline                   6.260736          12.521     0.5
 Gather F Bspline                   6.260736          75.129     3.1
 3D-FFT                            17.969344         143.755     6.0
 Solve PME                          0.326592          20.902     0.9
 NS-Pairs                          12.023515         252.494    10.5
 Reset In Box                       0.032608           0.098     0.0
 Shift-X                            0.097824           0.587     0.0
 CG-CoM                             0.097824           0.293     0.0
 Virial                             0.099264           1.787     0.1
 Settle                             0.065216          21.065     0.9
-----------------------------------------------------------------------
 Total                                              2413.698   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

 Computing:         Nodes     Number     G-Cycles    Seconds     %
-----------------------------------------------------------------------
 Neighbor search        2         32        1.272        0.4    35.2
 Force                  2         32        1.669        0.5    46.2
 PME mesh               2         32        0.405        0.1    11.2
 Constraints            2         63        0.218        0.1     6.1
 Rest                   2                   0.045        0.0     1.3
-----------------------------------------------------------------------
 Total                  1                   3.610        1.0   100.0
-----------------------------------------------------------------------

	Parallel run - timing based on wallclock.

               NODE (s)   Real (s)      (%)
       Time:      1.000      1.000    100.0
               (Mnbf/s)   (GFlops)   (steps/hour)
Performance:      4.873      2.414       115200.0
Finished mdrun on node 0 Fri Apr 24 17:59:11 2009