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

                   Good gRace! Old Maple Actually Chews Slate

                            :-)  VERSION 4.6.5  (-:

        Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, 
           Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,  
     Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, 
        Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, 
           Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, 
                Michael Shirts, Alfons Sijbers, Peter Tieleman,

               Berk Hess, David van der Spoel, and Erik Lindahl.

       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
         Copyright (c) 2001-2012,2013, The GROMACS development team at
        Uppsala University & The Royal Institute of Technology, Sweden.
            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 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.

                              :-)  grompp_mpi  (-:

Option     Filename  Type         Description
------------------------------------------------------------
  -f    dynamic.mdp  Input        grompp input file with MD parameters
 -po      mdout.mdp  Output       grompp input file with MD parameters
  -c equilibration.gro  Input        Structure file: gro g96 pdb tpr etc.
  -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
 -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
  -n      index.ndx  Input, Opt.  Index file
  -p     system.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o    dynamic.tpr  Output       Run input file: tpr tpb tpa
  -t equilibration.trr  Input, Opt!  Full precision trajectory: trr trj cpt
  -e       ener.edr  Input, Opt.  Energy file
-ref     rotref.trr  In/Out, Opt. Full precision trajectory: trr trj cpt

Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   no      Print help info and quit
-[no]version bool   no      Print version info and quit
-nice        int    0       Set the nicelevel
-[no]v       bool   no      Be loud and noisy
-time        real   -1      Take frame at or first after this time.
-[no]rmvsbds bool   yes     Remove constant bonded interactions with virtual
                            sites
-maxwarn     int    10      Number of allowed warnings during input
                            processing. Not for normal use and may generate
                            unstable systems
-[no]zero    bool   no      Set parameters for bonded interactions without
                            defaults to zero instead of generating an error
-[no]renum   bool   yes     Renumber atomtypes and minimize number of
                            atomtypes

Replacing old mdp entry 'unconstrained_start' by 'continuation'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#

NOTE 1 [file dynamic.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy


NOTE 2 [file dynamic.mdp]:
  The switch/shift interaction settings are just for compatibility; you
  will get better performance from applying potential modifiers to your
  interactions!



NOTE 3 [file dynamic.mdp]:
  For energy conservation with switch/shift potentials, rlist should be 0.1
  to 0.3 nm larger than rvdw.

Generated 1 of the 741 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'Protein_A'
Excluding 1 bonded neighbours molecule type 'POPC'
Excluding 1 bonded neighbours molecule type 'PW'

-------------------------------------------------------
Program grompp_mpi, VERSION 4.6.5
Source code file: /work/aoltu/build/gromacs-4.6.5/src/gmxlib/futil.c, line: 593

File input/output error:
equilibration.gro
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"You Don't Wanna Know" (Pulp Fiction)