<commit_before><tags>
  
  <item><name>cg</name><desc> Head option, which contains all coarse-graining options</desc></item>
  <item>
    <name>cg.non-bonded</name>
    <desc>
      Section for a non-bonded interaction. Most of the items in here are identical to items in cg.bonded,
      so they will be described in the same section.
    </desc>
  </item>
  <item>
    <name>cg.bonded</name>
    <desc>
      Section for a bonded interaction. Most of the items in here are identical to items in cg.bonded,
      so they will be described in the same section.
    </desc>
  </item>

<!-- general inverse options -->
  <item>
    <name>cg.inverse</name><section/>
    <desc>
      general options for inverse script
    </desc>
  </item>
  

  <item>
    <name>cg.inverse.cgmap</name>
    <desc>
      This option currently only has to be provided for IMC. It specifies the mapping file for
      analysis. Currently also during coarse-grained simulations, a mapping file has to be specified
      which is only a 1:1 mapping. This will change in the future.
    </desc>
  </item>
  <item><name>cg.inverse.kBT</name><desc> kBT (300*0.00831451 gromacs units) </desc></item>
  <item><name>cg.inverse.program</name><desc>simulation package to be used (currently only gromacs) </desc></item>

  <item><name>cg.inverse.$sim_prog</name><desc> generic simulation program (e.g. GROMACS) options </desc></item>
  <item><name>cg.inverse.$sim_prog.equi_time</name><default>0.0</default><desc> begin analysis after this time </desc></item>
  <item><name>cg.inverse.$sim_prog.first_frame</name><default>0</default><desc> trash so many frames at the beginning </desc></item>
  <item><name>cg.inverse.$sim_prog.topol</name><desc> topology + trajectory. Be careful, do not change yet! </desc></item>
  <item><name>cg.inverse.$sim_prog.traj</name><desc> topology + trajectory. Be careful, do not change yet! </desc></item>

  <item><name>cg.inverse.gromacs</name><desc> gromacs specific options </desc></item>
  <item><name>cg.inverse.gromacs.equi_time</name><default>0.0</default><desc> begin analysis after this time when using gromacs</desc></item><commit_msg>added option to xml<commit_after><tags>
  
  <item><name>cg</name><desc> Head option, which contains all coarse-graining options</desc></item>
  <item>
    <name>cg.non-bonded</name>
    <desc>
      Section for a non-bonded interaction. Most of the items in here are identical to items in cg.bonded,
      so they will be described in the same section.
    </desc>
  </item>
  <item>
    <name>cg.bonded</name>
    <desc>
      Section for a bonded interaction. Most of the items in here are identical to items in cg.bonded,
      so they will be described in the same section.
    </desc>
  </item>
  
  <item>
    <name>cg.nbsearch</name>
    <desc>
      Grid search algorithm, can be simple or grid. Default is simple.
    </desc>
  </item>

<!-- general inverse options -->
  <item>
    <name>cg.inverse</name><section/>
    <desc>
      general options for inverse script
    </desc>
  </item>
  

  <item>
    <name>cg.inverse.cgmap</name>
    <desc>
      This option currently only has to be provided for IMC. It specifies the mapping file for
      analysis. Currently also during coarse-grained simulations, a mapping file has to be specified
      which is only a 1:1 mapping. This will change in the future.
    </desc>
  </item>
  <item><name>cg.inverse.kBT</name><desc> kBT (300*0.00831451 gromacs units) </desc></item>
  <item><name>cg.inverse.program</name><desc>simulation package to be used (currently only gromacs) </desc></item>

  <item><name>cg.inverse.$sim_prog</name><desc> generic simulation program (e.g. GROMACS) options </desc></item>
  <item><name>cg.inverse.$sim_prog.equi_time</name><default>0.0</default><desc> begin analysis after this time </desc></item>
  <item><name>cg.inverse.$sim_prog.first_frame</name><default>0</default><desc> trash so many frames at the beginning </desc></item>
  <item><name>cg.inverse.$sim_prog.topol</name><desc> topology + trajectory. Be careful, do not change yet! </desc></item>
  <item><name>cg.inverse.$sim_prog.traj</name><desc> topology + trajectory. Be careful, do not change yet! </desc></item>

  <item><name>cg.inverse.gromacs</name><desc> gromacs specific options </desc></item>
  <item><name>cg.inverse.gromacs.equi_time</name><default>0.0</default><desc> begin analysis after this time when using gromacs</desc></item>
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