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equilP.log

.log file under discussion - Mark Abraham, 09/01/2010 11:04 AM

 
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Log file opened on Wed Sep  1 17:15:17 2010
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Host: v1253  pid: 24938  nodeid: 0  nnodes:  16
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The Gromacs distribution was built Tue Aug 31 09:43:09 EST 2010 by
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mxa224@vayu1 (Linux 2.6.27.49-1.8.3a x86_64)
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                         :-)  G  R  O  M  A  C  S  (-:
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                     Gnomes, ROck Monsters And Chili Sauce
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                  :-)  VERSION 4.5-beta4-20100826-54049cf  (-:
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      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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             Copyright (c) 2001-2008, The GROMACS development team,
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            check out http://www.gromacs.org for more information.
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         This program is free software; you can redistribute it and/or
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          modify it under the terms of the GNU General Public License
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         as published by the Free Software Foundation; either version 2
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             of the License, or (at your option) any later version.
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             :-)  /home/224/mxa224/progs/bin/mdrun_mpi_master  (-:
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
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molecular simulation
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J. Chem. Theory Comput. 4 (2008) pp. 435-447
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-------- -------- --- Thank You --- -------- --------
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34

    
35
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
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Berendsen
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GROMACS: Fast, Flexible and Free
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J. Comp. Chem. 26 (2005) pp. 1701-1719
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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E. Lindahl and B. Hess and D. van der Spoel
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GROMACS 3.0: A package for molecular simulation and trajectory analysis
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J. Mol. Mod. 7 (2001) pp. 306-317
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-------- -------- --- Thank You --- -------- --------
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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H. J. C. Berendsen, D. van der Spoel and R. van Drunen
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GROMACS: A message-passing parallel molecular dynamics implementation
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Comp. Phys. Comm. 91 (1995) pp. 43-56
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-------- -------- --- Thank You --- -------- --------
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Input Parameters:
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   integrator           = md
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   nsteps               = 1000
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   init_step            = 1000
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   ns_type              = Grid
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   nstlist              = 10
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   ndelta               = 2
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   nstcomm              = 10
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   comm_mode            = Linear
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   nstlog               = 100
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   nstxout              = 0
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   nstvout              = 0
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   nstfout              = 0
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   nstcalcenergy        = 10
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   nstenergy            = 0
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   nstxtcout            = 5000
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   init_t               = 0
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   delta_t              = 0.002
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   xtcprec              = 1000
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   nkx                  = 160
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   nky                  = 160
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   nkz                  = 160
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   pme_order            = 4
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   ewald_rtol           = 1e-05
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   ewald_geometry       = 0
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   epsilon_surface      = 0
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   optimize_fft         = FALSE
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   ePBC                 = xyz
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   bPeriodicMols        = FALSE
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   bContinuation        = TRUE
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   bShakeSOR            = FALSE
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   etc                  = Berendsen
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   nsttcouple           = 10
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   epc                  = Berendsen
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   epctype              = Isotropic
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   nstpcouple           = 10
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   tau_p                = 2
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   ref_p (3x3):
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      ref_p[    0]={ 1.00000e+00,  0.00000e+00,  0.00000e+00}
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      ref_p[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
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      ref_p[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}
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   compress (3x3):
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      compress[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
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      compress[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
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      compress[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
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   refcoord_scaling     = No
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   posres_com (3):
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      posres_com[0]= 0.00000e+00
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      posres_com[1]= 0.00000e+00
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      posres_com[2]= 0.00000e+00
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   posres_comB (3):
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      posres_comB[0]= 0.00000e+00
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      posres_comB[1]= 0.00000e+00
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      posres_comB[2]= 0.00000e+00
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   andersen_seed        = 815131
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   rlist                = 1
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   rlistlong            = 1
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   rtpi                 = 0.05
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   coulombtype          = PME
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   rcoulomb_switch      = 0
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   rcoulomb             = 1
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   vdwtype              = Cut-off
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   rvdw_switch          = 1
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   rvdw                 = 1
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   epsilon_r            = 1
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   epsilon_rf           = 1
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   tabext               = 1
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   implicit_solvent     = No
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   gb_algorithm         = Still
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   gb_epsilon_solvent   = 80
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   nstgbradii           = 1
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   rgbradii             = 2
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   gb_saltconc          = 0
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   gb_obc_alpha         = 1
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   gb_obc_beta          = 0.8
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   gb_obc_gamma         = 4.85
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   gb_dielectric_offset = 0.009
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   sa_algorithm         = No
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   sa_surface_tension   = 2.092
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   DispCorr             = EnerPres
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   free_energy          = no
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   init_lambda          = 0
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   delta_lambda         = 0
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   n_foreign_lambda     = 0
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   sc_alpha             = 0
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   sc_power             = 0
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   sc_sigma             = 0.3
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   sc_sigma_min         = 0.3
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   nstdhdl              = 10
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   separate_dhdl_file   = yes
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   dhdl_derivatives     = yes
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   dh_hist_size         = 0
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   dh_hist_spacing      = 0.1
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   nwall                = 0
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   wall_type            = 9-3
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   wall_atomtype[0]     = -1
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   wall_atomtype[1]     = -1
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   wall_density[0]      = 0
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   wall_density[1]      = 0
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   wall_ewald_zfac      = 3
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   pull                 = no
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   disre                = No
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   disre_weighting      = Conservative
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   disre_mixed          = FALSE
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   dr_fc                = 1000
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   dr_tau               = 0
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   nstdisreout          = 100
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   orires_fc            = 0
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   orires_tau           = 0
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   nstorireout          = 100
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   dihre-fc             = 1000
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   em_stepsize          = 0.01
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   em_tol               = 2000
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   niter                = 20
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   fc_stepsize          = 0
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   nstcgsteep           = 1000
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   nbfgscorr            = 10
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   ConstAlg             = Lincs
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   shake_tol            = 0.0001
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   lincs_order          = 4
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   lincs_warnangle      = 30
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   lincs_iter           = 6
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   bd_fric              = 0
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   ld_seed              = 1993
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   cos_accel            = 0
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   deform (3x3):
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      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
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   userint1             = 0
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   userint2             = 0
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   userint3             = 0
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   userint4             = 0
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   userreal1            = 0
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   userreal2            = 0
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   userreal3            = 0
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   userreal4            = 0
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grpopts:
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   nrdf:      390191
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   ref_t:         298
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   tau_t:         0.1
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anneal:          No
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ann_npoints:           0
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   acc:	           0           0           0
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   nfreeze:           N           N           N
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   energygrp_flags[  0]: 0
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   efield-x:
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      n = 0
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   efield-xt:
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      n = 0
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   efield-y:
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      n = 0
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   efield-yt:
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      n = 0
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   efield-z:
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      n = 0
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   efield-zt:
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      n = 0
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   bQMMM                = FALSE
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   QMconstraints        = 0
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   QMMMscheme           = 0
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   scalefactor          = 1
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qm_opts:
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   ngQM                 = 0
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Reading checkpoint file equilV.cpt
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  file generated by:     /home/224/mxa224/progs/bin/mdrun_mpi_master
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  file generated at:     Wed Sep  1 17:05:50 2010
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  GROMACS build time:    Tue Aug 31 09:43:09 EST 2010
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  GROMACS build user:    mxa224@vayu1
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  GROMACS build machine: Linux 2.6.27.49-1.8.3a x86_64
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  simulation part #:     -2
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  step:                  1000
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  time:                  2.000000
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State entry mismatch between the simulation and the checkpoint file
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Entries which are not present in the checkpoint file will not be updated
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                               simulation     checkpoint
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                       box      present        present  
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                   box-rel      present      not present
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                 pres_prev      present      not present
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                         x      present        present  
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                         v      present        present  
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Initializing Domain Decomposition on 16 nodes
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Dynamic load balancing: auto
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Will sort the charge groups at every domain (re)decomposition
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Initial maximum inter charge-group distances:
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    two-body bonded interactions: 0.433 nm, LJ-14, atoms 23013 23021
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  multi-body bonded interactions: 0.433 nm, Proper Dih., atoms 23013 23021
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Minimum cell size due to bonded interactions: 0.477 nm
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Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.819 nm
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Estimated maximum distance required for P-LINCS: 0.819 nm
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This distance will limit the DD cell size, you can override this with -rcon
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Domain decomposition grid 3 x 3 x 1, separate PME nodes 7
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PME domain decomposition: 7 x 1 x 1
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Interleaving PP and PME nodes
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This is a particle-particle only node
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Domain decomposition nodeid 0, coordinates 0 0 0
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Using two step summing over 2 groups of on average 4.5 processes
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Table routines are used for coulomb: TRUE
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Table routines are used for vdw:     FALSE
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Will do PME sum in reciprocal space.
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
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A smooth particle mesh Ewald method
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J. Chem. Phys. 103 (1995) pp. 8577-8592
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-------- -------- --- Thank You --- -------- --------
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Will do ordinary reciprocal space Ewald sum.
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Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
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Cut-off's:   NS: 1   Coulomb: 1   LJ: 1
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Long Range LJ corr.: <C6> 4.7219e-04
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System total charge: 0.000
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Generated table with 1000 data points for Ewald.
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Tabscale = 500 points/nm
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Generated table with 1000 data points for LJ6.
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Tabscale = 500 points/nm
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Generated table with 1000 data points for LJ12.
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Tabscale = 500 points/nm
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Generated table with 1000 data points for 1-4 COUL.
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Tabscale = 500 points/nm
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Generated table with 1000 data points for 1-4 LJ6.
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Tabscale = 500 points/nm
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Generated table with 1000 data points for 1-4 LJ12.
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Tabscale = 500 points/nm
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Enabling SPC-like water optimization for 40395 molecules.
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Configuring nonbonded kernels...
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Configuring standard C nonbonded kernels...
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Testing x86_64 SSE support... present.
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Initializing Parallel LINear Constraint Solver
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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B. Hess
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P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
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J. Chem. Theory Comput. 4 (2008) pp. 116-122
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-------- -------- --- Thank You --- -------- --------
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The number of constraints is 75232
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There are inter charge-group constraints,
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will communicate selected coordinates each lincs iteration
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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S. Miyamoto and P. A. Kollman
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SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
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Water Models
313
J. Comp. Chem. 13 (1992) pp. 952-962
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-------- -------- --- Thank You --- -------- --------
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Linking all bonded interactions to atoms
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There are 405888 inter charge-group exclusions,
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will use an extra communication step for exclusion forces for PME
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The initial number of communication pulses is: X 1 Y 1
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The initial domain decomposition cell size is: X 5.02 nm Y 4.89 nm
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The maximum allowed distance for charge groups involved in interactions is:
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                 non-bonded interactions           1.000 nm
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(the following are initial values, they could change due to box deformation)
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            two-body bonded interactions  (-rdd)   1.000 nm
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          multi-body bonded interactions  (-rdd)   1.000 nm
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  atoms separated by up to 5 constraints  (-rcon)  4.890 nm
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When dynamic load balancing gets turned on, these settings will change to:
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The maximum number of communication pulses is: X 1 Y 1
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The minimum size for domain decomposition cells is 1.000 nm
334
The requested allowed shrink of DD cells (option -dds) is: 0.80
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The allowed shrink of domain decomposition cells is: X 0.20 Y 0.20
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The maximum allowed distance for charge groups involved in interactions is:
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                 non-bonded interactions           1.000 nm
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            two-body bonded interactions  (-rdd)   1.000 nm
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          multi-body bonded interactions  (-rdd)   1.000 nm
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  atoms separated by up to 5 constraints  (-rcon)  1.000 nm
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Making 2D domain decomposition grid 3 x 3 x 1, home cell index 0 0 0
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Center of mass motion removal mode is Linear
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We have the following groups for center of mass motion removal:
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  0:  rest
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++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
351
Molecular dynamics with coupling to an external bath
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J. Chem. Phys. 81 (1984) pp. 3684-3690
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-------- -------- --- Thank You --- -------- --------
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There are: 195537 Atoms
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Charge group distribution at step 1000: 2246 13527 12032 13879 31333 14005 11890 13637 2198
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Grid: 15 x 15 x 15 cells
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Initial temperature: 300.136 K
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Started mdrun on node 0 Wed Sep  1 17:15:19 2010
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           Step           Time         Lambda
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           1000        2.00000        0.00000
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   Energies (kJ/mol)
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          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
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    1.27775e+05    2.01100e+05    7.98928e+03    8.07423e+04    8.47474e+05
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        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
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    3.23727e+04   -8.47086e+03   -1.99198e+06   -1.32540e+06   -2.02840e+06
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    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
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    4.86757e+05   -1.54165e+06    3.00074e+02   -6.30235e+01   -1.91051e+02
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   Constr. rmsd
373
    3.16975e-06
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DD  step 1009 load imb.: force 172.1%  pme mesh/force 0.528
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At step 1010 the performance loss due to force load imbalance is 35.5 %
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NOTE: Turning on dynamic load balancing
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DD  load balancing is limited by minimum cell size in dimension Y
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DD  step 1099  vol min/aver 0.417! load imb.: force 16.2%  pme mesh/force 1.215
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           Step           Time         Lambda
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           1100        2.20000        0.00000
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   Energies (kJ/mol)
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          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
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    1.28638e+05    2.01095e+05    8.06873e+03    8.06054e+04    8.47354e+05
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        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
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    3.80304e+04   -8.47694e+03   -2.00319e+06   -1.32564e+06   -2.03352e+06
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    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
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    4.86405e+05   -1.54711e+06    2.99857e+02   -6.31141e+01   -9.56536e+01
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   Constr. rmsd
395
    3.17637e-06
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DD  load balancing is limited by minimum cell size in dimension Y
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DD  step 1199  vol min/aver 0.398! load imb.: force 10.9%  pme mesh/force 1.282
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           Step           Time         Lambda
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           1200        2.40000        0.00000
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   Energies (kJ/mol)
404
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
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    1.28431e+05    2.00901e+05    8.13355e+03    8.10133e+04    8.48169e+05
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        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
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    3.57556e+04   -8.48096e+03   -2.00636e+06   -1.32607e+06   -2.03851e+06
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    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
409
    4.85976e+05   -1.55254e+06    2.99593e+02   -6.31740e+01   -5.38952e+01
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   Constr. rmsd
411
    3.16764e-06
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DD  load balancing is limited by minimum cell size in dimension Y
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DD  step 1299  vol min/aver 0.396! load imb.: force 10.7%  pme mesh/force 1.282
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           Step           Time         Lambda
417
           1300        2.60000        0.00000
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   Energies (kJ/mol)
420
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
421
    1.28506e+05    2.01210e+05    8.40823e+03    8.09022e+04    8.48167e+05
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        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
423
    3.92211e+04   -8.48256e+03   -2.01604e+06   -1.32665e+06   -2.04476e+06
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    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
425
    4.87206e+05   -1.55755e+06    3.00350e+02   -6.31978e+01    1.41008e+00
426
   Constr. rmsd
427
    3.16231e-06
428

    
429
DD  load balancing is limited by minimum cell size in dimension Y
430
DD  step 1399  vol min/aver 0.397! load imb.: force 10.8%  pme mesh/force 1.278
431

    
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           Step           Time         Lambda
433
           1400        2.80000        0.00000
434

    
435
   Energies (kJ/mol)
436
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
437
    1.28926e+05    2.01088e+05    8.45534e+03    8.08407e+04    8.47643e+05
438
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
439
    4.00276e+04   -8.48205e+03   -2.02008e+06   -1.32669e+06   -2.04827e+06
440
    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
441
    4.86022e+05   -1.56225e+06    2.99621e+02   -6.31902e+01    8.81758e+00
442
   Constr. rmsd
443
    3.16657e-06
444

    
445
DD  load balancing is limited by minimum cell size in dimension Y
446
DD  step 1499  vol min/aver 0.395! load imb.: force 10.7%  pme mesh/force 1.278
447

    
448
           Step           Time         Lambda
449
           1500        3.00000        0.00000
450

    
451
   Energies (kJ/mol)
452
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
453
    1.30607e+05    2.01198e+05    8.25554e+03    8.09889e+04    8.48433e+05
454
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
455
    3.65495e+04   -8.48126e+03   -2.02054e+06   -1.32698e+06   -2.04997e+06
456
    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
457
    4.83988e+05   -1.56598e+06    2.98367e+02   -6.31784e+01    1.68905e+01
458
   Constr. rmsd
459
    3.16242e-06
460

    
461
DD  load balancing is limited by minimum cell size in dimension Y
462
DD  step 1599  vol min/aver 0.394! load imb.: force 10.8%  pme mesh/force 1.274
463

    
464
           Step           Time         Lambda
465
           1600        3.20000        0.00000
466

    
467
   Energies (kJ/mol)
468
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
469
    1.29226e+05    2.01529e+05    8.22719e+03    8.12233e+04    8.48413e+05
470
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
471
    3.71381e+04   -8.47962e+03   -2.02412e+06   -1.32716e+06   -2.05400e+06
472
    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
473
    4.85986e+05   -1.56802e+06    2.99598e+02   -6.31539e+01    9.31526e+01
474
   Constr. rmsd
475
    3.17172e-06
476

    
477
DD  load balancing is limited by minimum cell size in dimension Y
478
DD  step 1699  vol min/aver 0.392! load imb.: force 10.8%  pme mesh/force 1.276
479

    
480
           Step           Time         Lambda
481
           1700        3.40000        0.00000
482

    
483
   Energies (kJ/mol)
484
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
485
    1.29748e+05    2.02001e+05    8.35743e+03    8.13689e+04    8.47770e+05
486
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
487
    4.06192e+04   -8.47566e+03   -2.03012e+06   -1.32714e+06   -2.05588e+06
488
    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
489
    4.84615e+05   -1.57126e+06    2.98754e+02   -6.30949e+01    1.80609e+02
490
   Constr. rmsd
491
    3.14991e-06
492

    
493
DD  load balancing is limited by minimum cell size in dimension Y
494
DD  step 1799  vol min/aver 0.391! load imb.: force 10.9%  pme mesh/force 1.272
495

    
496
           Step           Time         Lambda
497
           1800        3.60000        0.00000
498

    
499
   Energies (kJ/mol)
500
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
501
    1.31511e+05    2.01338e+05    8.31839e+03    8.12051e+04    8.47704e+05
502
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
503
    3.93847e+04   -8.46977e+03   -2.03266e+06   -1.32743e+06   -2.05910e+06
504
    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
505
    4.84679e+05   -1.57442e+06    2.98793e+02   -6.30073e+01    1.54197e+02
506
   Constr. rmsd
507
    3.16934e-06
508

    
509
DD  load balancing is limited by minimum cell size in dimension Y
510
DD  step 1899  vol min/aver 0.390! load imb.: force 10.8%  pme mesh/force 1.273
511

    
512
           Step           Time         Lambda
513
           1900        3.80000        0.00000
514

    
515
   Energies (kJ/mol)
516
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
517
    1.30906e+05    2.01670e+05    8.51058e+03    8.15619e+04    8.48236e+05
518
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
519
    3.80666e+04   -8.46388e+03   -2.03374e+06   -1.32759e+06   -2.06084e+06
520
    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
521
    4.83644e+05   -1.57719e+06    2.98155e+02   -6.29198e+01    1.97077e+02
522
   Constr. rmsd
523
    3.15474e-06
524

    
525
DD  load balancing is limited by minimum cell size in dimension Y
526
DD  step 1999  vol min/aver 0.389! load imb.: force 10.8%  pme mesh/force 1.272
527

    
528
           Step           Time         Lambda
529
           2000        4.00000        0.00000
530

    
531
Writing checkpoint, step 2000 at Wed Sep  1 17:18:19 2010
532

    
533

    
534
   Energies (kJ/mol)
535
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
536
    1.31210e+05    2.01448e+05    8.25925e+03    8.12783e+04    8.46918e+05
537
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
538
    3.82007e+04   -8.45747e+03   -2.03562e+06   -1.32723e+06   -2.06399e+06
539
    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
540
    4.84978e+05   -1.57901e+06    2.98977e+02   -6.28245e+01    1.91142e+02
541
   Constr. rmsd
542
    3.17026e-06
543