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<cg>
<!-- example for a non-bonded interaction entry -->
<non-bonded>
<!-- name of the interaction -->
<name>CG-CG</name>
<!-- types involved in this interaction -->
<type1>CG</type1>
<type2>CG</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0</min>
<max>0.9</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromacs rdf.xvg -->
<target>CG-CG.dist.tgt</target>
<!-- update cycles -->
<do_potential>1</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_update>smooth</post_update>
<!-- some options for the post update scripts -->
<post_update_options>
<splinesmooth>
<step>0.02</step>
</splinesmooth>
<smooth>
<iterations>4</iterations>
</smooth>
</post_update_options>
<!-- additional post processing of U after dU added to potential -->
<post_add>acc_convergence plot</post_add>
<post_add_options>
<copyback>
<filelist>${name}.pot.new ${name}.dpot.new ${name}.dist.new</filelist>
</copyback>
<convergence>
<weight>0.2</weight>
<what>dist</what>
</convergence>
<plot>
<script>allplots.gp</script>
<kill>gnuplot_x11</kill>
<gnuplot_opts>-geometry 1024x700 -persist</gnuplot_opts>
</plot>
</post_add_options>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_CG_CG.xvg</table>
</gromacs>
<!-- inverse monte carlo specific stuff -->
</inverse>
</non-bonded>
<!-- general options for inverse script -->
<inverse>
<!-- 300*0.00831451 gromacs units -->
<kBT>2.49435</kBT>
<!-- use gromacs as simulation program -->
<program>gromacs</program>
<!-- gromacs specific options -->
<gromacs>
<!-- trash so many frames at the beginning -->
<equi_time>1</equi_time>
<!-- grid for table*.xvg !-->
<table_bins>0.002</table_bins>
<!-- cut the potential at this value (gromacs bug) -->
<pot_max>1000000</pot_max>
<!-- extend the tables to this value -->
<table_end>2.0</table_end>
</gromacs>
<!-- these files are copied for each new run -->
<filelist>grompp.mdp topol.top table.xvg index.ndx allplots.gp</filelist>
<!-- do so many iterations -->
<iterations_max>300</iterations_max>
<!-- ibm: inverse boltzmann imc: inverse monte carlo -->
<method>ibi</method>
</inverse>
</cg>
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