Hi, Justin Sorry for the unclear message. My box vector in .gro file are 44.22834  44.22834  44.22834 and the number of atoms is 20171 The output of grompp is shown below, I don't know if it is enough and I'm sorry I don't know how should I do after you reply. Could you please give me more messages in detail?
Hsin-Lin -----------------------------------------------------------         Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,       Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,         Gerrit Groenhof, Peter Kasson, 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) 2001-2010, 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 General Public License          as published by the Free Software Foundation; either version 2              of the License, or (at your option) any later version.                                 :-)  grompp  (-: Option     Filename  Type         Description ------------------------------------------------------------   -f       test.mdp  Input        grompp input file with MD parameters  -po      mdout.mdp  Output       grompp input file with MD parameters   -c  ../3eq/eq.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 ../initial/index.ndx  Input, Opt!  Index file   -p ../initial/insulin.top  Input        Topology file  -pp  processed.top  Output, Opt. Topology file   -o       test.tpr  Output       Run input file: tpr tpb tpa   -t  ../3eq/eq.trr  Input, Opt!  Full precision trajectory: trr trj cpt   -e       ener.edr  Input, Opt.  Energy file 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    0       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 Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA' turning H bonds into constraints... Velocities were taken from a Maxwell distribution at 300 K Number of degrees of freedom in T-Coupling group Protein is 1448.89 Number of degrees of freedom in T-Coupling group non-Protein is 39297.11 Reading Coordinates and Box size from old trajectory Will read whole trajectory Velocities generated: ignoring velocities in input trajectory trn version: GMX_trn_file (single precision) Last frame        800 time  800.000 Using frame at t = 800 ps Starting time for run is 0 ps Largest charge group radii for Van der Waals: 0.248, 0.178 nm Largest charge group radii for Coulomb:       0.248, 0.214 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 224x224x224, spacing 0.197 0.197 0.197 Estimate for the relative computational load of the PME mesh part: 1.00 NOTE 1 [file test.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 2 [file test.mdp]:   This run will generate roughly 3481 Mb of data There were 2 notes Back Off! I just backed up test.tpr to ./#test.tpr.3# gcq#159: "Way to Go Dude" (Beavis and Butthead)
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