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<font size="2">Hi, Justin
<br />
<br />Sorry for the unclear message.
<br />My box vector in .gro file are 44.22834  44.22834  44.22834 and the number of atoms is 20171
<br />The output of grompp is shown below,
<br />I don't know if it is enough and I'm sorry I don't know how should I do after you reply.
<br />Could you please give me more messages in detail?
<br />
<br />Hsin-Lin
<br />-----------------------------------------------------------
<br />        Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
<br />      Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
<br />        Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
<br />           Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
<br />                Michael Shirts, Alfons Sijbers, Peter Tieleman,
<br />
<br />               Berk Hess, David van der Spoel, and Erik Lindahl.
<br />
<br />       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
<br />            Copyright (c) 2001-2010, The GROMACS development team at
<br />        Uppsala University & The Royal Institute of Technology, Sweden.
<br />            check out http://www.gromacs.org for more information.
<br />
<br />         This program is free software; you can redistribute it and/or
<br />          modify it under the terms of the GNU General Public License
<br />         as published by the Free Software Foundation; either version 2
<br />             of the License, or (at your option) any later version.
<br />
<br />                                :-)  grompp  (-:
<br />
<br />Option     Filename  Type         Description
<br />------------------------------------------------------------
<br />  -f       test.mdp  Input        grompp input file with MD parameters
<br /> -po      mdout.mdp  Output       grompp input file with MD parameters
<br />  -c  ../3eq/eq.gro  Input        Structure file: gro g96 pdb tpr etc.
<br />  -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
<br /> -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
<br />  -n ../initial/index.ndx  Input, Opt!  Index file
<br />  -p ../initial/insulin.top  Input        Topology file
<br /> -pp  processed.top  Output, Opt. Topology file
<br />  -o       test.tpr  Output       Run input file: tpr tpb tpa
<br />  -t  ../3eq/eq.trr  Input, Opt!  Full precision trajectory: trr trj cpt
<br />  -e       ener.edr  Input, Opt.  Energy file
<br />
<br />Option       Type   Value   Description
<br />------------------------------------------------------
<br />-[no]h       bool   no      Print help info and quit
<br />-[no]version bool   no      Print version info and quit
<br />-nice        int    0       Set the nicelevel
<br />-[no]v       bool   no      Be loud and noisy
<br />-time        real   -1      Take frame at or first after this time.
<br />-[no]rmvsbds bool   yes     Remove constant bonded interactions with virtual
<br />                            sites
<br />-maxwarn     int    0       Number of allowed warnings during input
<br />                            processing. Not for normal use and may generate
<br />                            unstable systems
<br />-[no]zero    bool   no      Set parameters for bonded interactions without
<br />                            defaults to zero instead of generating an error
<br />-[no]renum   bool   yes     Renumber atomtypes and minimize number of
<br />                            atomtypes
<br />
<br />Ignoring obsolete mdp entry 'title'
<br />Ignoring obsolete mdp entry 'cpp'
<br />
<br />Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
<br />Generated 279 of the 1225 non-bonded parameter combinations
<br />Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
<br />turning H bonds into constraints...
<br />Excluding 2 bonded neighbours molecule type 'SOL'
<br />turning H bonds into constraints...
<br />Excluding 1 bonded neighbours molecule type 'NA'
<br />turning H bonds into constraints...
<br />Velocities were taken from a Maxwell distribution at 300 K
<br />Number of degrees of freedom in T-Coupling group Protein is 1448.89
<br />Number of degrees of freedom in T-Coupling group non-Protein is 39297.11
<br />Reading Coordinates and Box size from old trajectory
<br />Will read whole trajectory
<br />Velocities generated: ignoring velocities in input trajectory
<br />trn version: GMX_trn_file (single precision)
<br />Last frame        800 time  800.000
<br />Using frame at t = 800 ps
<br />Starting time for run is 0 ps
<br />Largest charge group radii for Van der Waals: 0.248, 0.178 nm
<br />Largest charge group radii for Coulomb:       0.248, 0.214 nm
<br />Calculating fourier grid dimensions for X Y Z
<br />Using a fourier grid of 224x224x224, spacing 0.197 0.197 0.197
<br />Estimate for the relative computational load of the PME mesh part: 1.00
<br />
<br />NOTE 1 [file test.mdp]:
<br />  The optimal PME mesh load for parallel simulations is below 0.5
<br />  and for highly parallel simulations between 0.25 and 0.33,
<br />  for higher performance, increase the cut-off and the PME grid spacing
<br />
<br />
<br />NOTE 2 [file test.mdp]:
<br />  This run will generate roughly 3481 Mb of data
<br />
<br />There were 2 notes
<br />
<br />Back Off! I just backed up test.tpr to ./#test.tpr.3#
<br />
<br />gcq#159: "Way to Go Dude" (Beavis and Butthead)
<br />
<br />
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