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  10 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>grompp</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
  12 </TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
  13 Thu 26 Aug 2010</B></td></tr></TABLE>
  14 <HR>
  15 <H3>Description</H3>
  16 <p>
  17 The gromacs preprocessor
  18 reads a molecular topology file, checks the validity of the
  19 file, expands the topology from a molecular description to an atomic
  20 description. The topology file contains information about
  21 molecule types and the number of molecules, the preprocessor
  22 copies each molecule as needed.
  23 There is no limitation on the number of molecule types.
  24 Bonds and bond-angles can be converted into constraints, separately
  25 for hydrogens and heavy atoms.
  26 Then a coordinate file is read and velocities can be generated
  27 from a Maxwellian distribution if requested.
  28 grompp also reads parameters for the <a href="mdrun.html">mdrun</a>
  29 (eg. number of MD steps, time step, cut-off), and others such as
  30 NEMD parameters, which are corrected so that the net acceleration
  31 is zero.
  32 Eventually a binary file is produced that can serve as the sole input
  33 file for the MD program.<p>
  34 grompp uses the atom names from the topology file. The atom names
  35 in the coordinate file (option <tt>-c</tt>) are only read to generate
  36 warnings when they do not match the atom names in the topology.
  37 Note that the atom names are irrelevant for the simulation as
  38 only the atom types are used for generating interaction parameters.<p>
  39 grompp uses a built-in preprocessor to resolve includes, macros
  40 etcetera. The preprocessor supports the following keywords:<br>
  41 #ifdef VARIABLE<br>
  42 #ifndef VARIABLE<br>
  43 #else<br>
  44 #endif<br>
  45 #define VARIABLE<br>
  46 #undef VARIABLE<br>#include "filename"<br>
  47 #include &lt;filename&gt;<br>
  48 The functioning of these statements in your topology may be modulated by
  49 using the following two flags in your <tt><a href="mdp.html">mdp</a></tt> file:<br>
  50 define = -DVARIABLE1 -DVARIABLE2<br>
  51 include = /home/john/doe<br>
  52 For further information a C-programming textbook may help you out.
  53 Specifying the <tt>-pp</tt> flag will get the pre-processed
  54 topology file written out so that you can verify its contents.<p>
  55 If your system does not have a c-preprocessor, you can still
  56 use grompp, but you do not have access to the features
  57 from the cpp. Command line options to the c-preprocessor can be given
  58 in the <tt>.<a href="mdp.html">mdp</a></tt> file. See your local manual (man cpp).<p>
  59 When using position restraints a file with restraint coordinates
  60 can be supplied with <tt>-r</tt>, otherwise restraining will be done
  61 with respect to the conformation from the <tt>-c</tt> option.
  62 For free energy calculation the the coordinates for the B topology
  63 can be supplied with <tt>-rb</tt>, otherwise they will be equal to
  64 those of the A topology.<p>
  65 Starting coordinates can be read from trajectory with <tt>-t</tt>.
  66 The last frame with coordinates and velocities will be read,
  67 unless the <tt>-time</tt> option is used.
  68 Note that these velocities will not be used when <tt>gen_vel = yes</tt>
  69 in your <tt>.<a href="mdp.html">mdp</a></tt> file. An energy file can be supplied with
  70 <tt>-e</tt> to read Nose-Hoover and/or Parrinello-Rahman coupling
  71 variables. Note that for continuation it is better and easier to supply
  72 a checkpoint file directly to <a href="mdrun.html">mdrun</a>, since that always contains
  73 the complete state of the system and you don't need to generate
  74 a new run input file. Note that if you only want to change the number
  75 of run steps <a href="tpbconv.html">tpbconv</a> is more convenient than grompp.<p>
  76 Using the <tt>-morse</tt> option grompp can convert the harmonic bonds
  77 in your topology to morse potentials. This makes it possible to break
  78 bonds. For this option to work you need an extra file in your $GMXLIB
  79 with dissociation energy. Use the -debug option to get more information
  80 on the workings of this option (look for MORSE in the grompp.<a href="log.html">log</a> file
  81 using less or something like that).<p>
  82 By default all bonded interactions which have constant energy due to
  83 virtual site constructions will be removed. If this constant energy is
  84 not zero, this will result in a shift in the total energy. All bonded
  85 interactions can be kept by turning off <tt>-rmvsbds</tt>. Additionally,
  86 all constraints for distances which will be constant anyway because
  87 of virtual site constructions will be removed. If any constraints remain
  88 which involve virtual sites, a fatal error will result.<p>To verify your run input file, please make notice of all warnings
  89 on the screen, and correct where necessary. Do also look at the contents
  90 of the <tt>mdout.<a href="mdp.html">mdp</a></tt> file, this contains comment lines, as well as
  91 the input that <tt>grompp</tt> has read. If in doubt you can start grompp
  92 with the <tt>-debug</tt> option which will give you more information
  93 in a file called grompp.<a href="log.html">log</a> (along with real debug info). Finally, you
  94 can see the contents of the run input file with the <tt><a href="gmxdump.html">gmxdump</a></tt>
  95 program.
  96 <P>
  97 <H3>Files</H3>
  98 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  99 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
 100 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mdp.html">  grompp.mdp</a></tt> </TD><TD> Input, Opt. </TD><TD> grompp input file with MD parameters </TD></TR>
 101 <TR><TD ALIGN=RIGHT> <b><tt>-po</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mdp.html">   mdout.mdp</a></tt> </TD><TD> Output </TD><TD> grompp input file with MD parameters </TD></TR>
 102 <TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    conf.gro</a></tt> </TD><TD> Input </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> etc. </TD></TR>
 103 <TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    conf.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> etc. </TD></TR>
 104 <TR><TD ALIGN=RIGHT> <b><tt>-rb</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    conf.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> etc. </TD></TR>
 105 <TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
 106 <TR><TD ALIGN=RIGHT> <b><tt>-p</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="top.html">   topol.top</a></tt> </TD><TD> Input </TD><TD> Topology file </TD></TR>
 107 <TR><TD ALIGN=RIGHT> <b><tt>-pp</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="top.html">processed.top</a></tt> </TD><TD> Output, Opt. </TD><TD> Topology file </TD></TR>
 108 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   topol.tpr</a></tt> </TD><TD> Output </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
 109 <TR><TD ALIGN=RIGHT> <b><tt>-t</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    traj.trr</a></tt> </TD><TD> Input, Opt. </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
 110 <TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edr.html">    ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD> Energy file </TD></TR>
 111 </TABLE>
 112 <P>
 113 <H3>Other options</H3>
 114 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
 115 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
 116 <TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print help info and quit </TD></TD>
 117 <TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print version info and quit </TD></TD>
 118 <TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
 119 <TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Be loud and noisy </TD></TD>
 120 <TR><TD ALIGN=RIGHT> <b><tt>-time</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1    </tt> </TD><TD> Take frame at or first after this time. </TD></TD>
 121 <TR><TD ALIGN=RIGHT> <b><tt>-[no]rmvsbds</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Remove constant bonded interactions with virtual sites </TD></TD>
 122 <TR><TD ALIGN=RIGHT> <b><tt>-maxwarn</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of allowed warnings during input processing </TD></TD>
 123 <TR><TD ALIGN=RIGHT> <b><tt>-[no]zero</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Set parameters for bonded interactions without defaults to zero instead of generating an error </TD></TD>
 124 <TR><TD ALIGN=RIGHT> <b><tt>-[no]renum</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Renumber atomtypes and minimize number of atomtypes </TD></TD>
 125 </TABLE>
 126 <P>
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