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

                   Great Red Oystrich Makes All Chemists Sane

                            :-)  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.7#

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 'CHOL'
Excluding 1 bonded neighbours molecule type 'POPC'
Excluding 1 bonded neighbours molecule type 'CHOL'
Excluding 1 bonded neighbours molecule type 'PW'
Cleaning up constraints and constant bonded interactions with virtual sites
Cleaning up constraints and constant bonded interactions with virtual sites
Number of degrees of freedom in T-Coupling group Protein is 185.98
Number of degrees of freedom in T-Coupling group POPC_CHOL is 4593.45
Number of degrees of freedom in T-Coupling group PW is 20367.57
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory
trn version: GMX_trn_file (single precision)

Reading frame       0 time    0.000   
Reading frame       1 time  100.000   
Reading frame       2 time  200.000   
Reading frame       3 time  300.000   
Reading frame       4 time  400.000   
Reading frame       5 time  500.000   
Reading frame       6 time  600.000   
Reading frame       7 time  700.000   
Reading frame       8 time  800.000   
Reading frame       9 time  900.000   
Reading frame      10 time 1000.000   
Last frame         10 time 1000.000   
Using frame at t = 1000 ps
Starting time for run is 0 ps

NOTE 4 [file dynamic.mdp]:
  The sum of the two largest charge group radii (0.186244) is larger than
  rlist (1.200000) - rvdw (1.200000).
  With exact cut-offs, better performance can be obtained with
  cutoff-scheme = Verlet, because it does not use charge groups at all.

Estimate for the relative computational load of the PME mesh part: 0.61

NOTE 5 [file dynamic.mdp]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing.



NOTE 6 [file dynamic.mdp]:
  This run will generate roughly 4327 Mb of data


There were 6 notes

Back Off! I just backed up dynamic.tpr to ./#dynamic.tpr.1#

gcq#133: "Check Your Input" (D. Van Der Spoel)