Please mind that dots in xml tags have to replaced by subtags, e.g. x.y has to be converted to x with subtag y.
 cg Section containing the all coarsegraining options
 bonded Interaction specific option for bonded interactions, see the cg.nonbonded section for all options
 name Name of the bonded interaction. The name can be arbitrary but should be unique. For bonded interactions, this should match the name specified in the mapping file.
 fmatch Force matching options
 constrainedLS boolean variable: false  simple least squares, true  constrained least squares. For details see the VOTCA paper. Practically, both algorithms give the same results, but simple least squares is faster. If you are a mathematician and you think that a spline can only then be called a spline if it has continuous first and second derivatives, use constrained least squares.
 frames_per_block number of frames, being used for block averaging. Atomistic trajectory, specified with trj option, is divided into blocks and the force matching equations are solved separately for each block. Coarsegrained forcefield, which one gets on the output is averaged over those blocks.
 inverse general options for inverse script
 cleanlist these files are removed after each iteration
 convergence_check
 limit lower convergency limit to stop (default 0)
 type type of convergence check to do (default none)
 espresso
 blockfile Name of the original blockfile read by Espresso (default conf.esp.gz)
 blockfile_out Name of the original outcome blockfile written by Espresso (default confout.esp.gz)
 command Command to run espresso (name or absolute path or mpirun espresso..) (default Espresso)
 debug debug Espresso (yes/no) (default no)
 exclusions Espresso bond partners to exclude (default 0)
 first_frame trash the given number of frames at the beginning of trajectory (default 0)
 meta_cmd Espresso metadynamics command to call [experimental]
 meta_min_sampling Espresso metadynamics minimal number of sampling [experimental]
 n_snapshots number of snapshots. Total time = n_steps csg_defaults.xml.t2t Makefile Makefile.incl Makefile.XMLS xml2t2t.sh n_snapshots
 n_steps Number of steps to integrate before a snapshot
 pressure_command Espresso command to run when calculating the pressure (name or absolute path or mpirun espresso..) (default Espresso)
 rdf_command Espresso command to run when calculating the rdf (name or absolute path or mpirun espresso..) (default Espresso)
 scriptdir overwrite ESPRESSO_SCRIPTS from environment with this dir
 success File to create if Espresso simulation was successfull (default success.esp)
 table_bins espresso internal grid for tabulated potentials
 table_end end of espresso internal table
 traj Name of the output Espresso trajectory file (default top_traj.esp)
 filelist these files are copied to each iteration step
 gnuplot
 bin gnuplot binary to use (default gnuplot)
 gromacs gromacs specific options
 conf Name of the coordinate file read by grompp (default conf.gro)
 conf_out Name of the original outcome coordinate written by mdrun (default confout.gro)
 cutoff_check check nonbonded interaction cutoffs against rvdw in mdp file: yes/no (default yes)
 density
 density.block_length Length of the block for the error analysis
 density.with_errors calculate error on the density: yes/no (default no)
 equi_time begin analysis after this time when using gromacs (max of this and first_frame is used) (default 0)
 first_frame trash the given number of frames at the beginning of trajectory (max of this and first_frame is used) (default 0)
 g_energy
 g_energy.bin Name (or absolute path) of the g_energy binary (default g_energy)
 g_energy.opts Additional options to Gromacs g_energy (e.g. P 1)
 g_energy.pressure options for pressure calculation using g_energy
 g_energy.pressure.allow_nan is nan an allowed result: yes/no (default no)
 g_energy.topol Gromacs binary topol (tpr) file to use by g_energy
 gmxrc GMXRC to source at the startup
 grompp
 grompp.bin Name (or absolute path) of the grompp binary (default grompp)
 grompp.opts Additional options to Gromacs grompp (e.g. maxwarn 1)
 index Gromacs grompp index file to used by grompp (default index.ndx)
 log Separate log file for gromacs programs (useful with mdrun v)
 mdp Gromacs mdp file to be used by grompp (default grompp.mdp)
 mdrun
 mdrun.checkpoint Name of the checkpint to use in case of restarted simulation (default state.cpt)
 mdrun.command Command to run mdrun (name or absolute path or mpirun mdrun..) (default mdrun)
 mdrun.opts Additional options to Gromacs mdrun (e.g. nosum)
 pot_max cut the potential at this value (gromacs bug) (default 1000000)
 pre_simulation A pre simulation (e.g. minimization / equilibration ) is a simulation with a different mdp/topol/index (default no)
 pre_simulation.index Gromacs grompp index file to used by grompp in the pre simulation
 pre_simulation.mdp Gromacs mdp file to be used by grompp in the pre simulation
 pre_simulation.topol_in Gromacs text topol (top) file to use by grompp in the pre simulation
 rdf
 rdf.block_length Length of the block for the error analysis
 rdf.map Special mapping file for rdf calculations needed for bonded interactions
 rdf.topol Gromacs binary topol (tpr) file to be used for csg_stat
 rdf.with_errors calculate error on the rdf: yes/no (default no)
 ref Options for the case that calculation of reference system is needed
 ref.equi_time begin analysis after this time when using gromacs (max of this and first_frame is used) (default 0)
 ref.first_frame trash the given number of frames at the beginning of trajectory (max of this and first_frame is used) (default 0)
 ref.mapping Mapping to apply on the coarsegrained topology, use autogenerated ones (cg.inverse.optimizer.mapping.output) and given ones (map other components)
 ref.rdf Contains options for Reference rdf calculation
 ref.rdf.opts Extra options to give to csg_stat (e.g. nframes 100)
 ref.topol Reference binary topology(global or local path)
 ref.traj Reference trajectory(global or local path)
 table_bins grid for gromacs xvg table (default 0.002)
 table_end extend the gromacs xvg tables to this value
 temp_check check kBT against t_ref in mdp file: yes/no (default yes)
 topol_in Gromacs text topology (top) file read by grompp (default topol.top)
 topol_out Gromacs binary topology (tpr) file to be written by grompp and used for the simlation (default topol.tpr)
 traj_type Gromacs trajectory type (xtc/trr) file to use (default xtc)
 imc general imc specific options
 matlab
 matlab.bin Name (or absolute path) of the matlab binary (default matlab)
 numpy
 numpy.bin Name (or absolute path) of the python binary used by the numpy solver (default python)
 octave
 octave.bin Name (or absolute path) of the octave binary (default octave)
 solver solver for solving a linear equation system: octave/numpy/matlab
 initial_configuration what initial configuration to use in every step: maindir/laststep (default laststep)
 iterations_max do the given number of iterations (0=inf)
 kBT kBT in simulation progam units (XXX K *0.00831451 for gromacs)
 log_file name of the log file (default inverse.log)
 map Special mapping file for rdf calculations needed for bonded interactions
 method method to be performed: ibi/imc/ft/optimizer
 optimizer
 cma general options for the cma optimizer
 cma.eps standard epsilon, in which the best solution is searched
 type Type of optimizer to be used
 program simulation package to be used (gromacs/espresso) (default gromacs)
 restart_file Name of the restart file in case a step has to be resumed (default restart_points.log)
 scriptpath list of directories for user scripts (e.g. $PWD) separated by a colon (like PATH)
 simulation simulation options
 background tells csg_inverse that simulation was send to the backgroud (default no)
 tasks number of threads to use for csg_stat (default auto)
 nbsearch Grid search algorithm, simple (N square search) or grid (default grid)
 nonbonded Interaction specific option for nonbonded interactions
 bondtype Internal alias for "nonbonded" or "bonded", set automatically
 fmatch Force matching options
 max Maximum value of interval for distribution sampled in atomistic MD simulation. One can get this number by looking at the distribution function for this interaction. For nonbonded interactions it's the cutoff of the interaction.
 min Minimum value of interval for distribution sampled in atomistic MD simulation. One can get this number by looking at the distribution function for this interaction. For nonbonded interactions it's the distance to the rdf start. For CG bonds and angles the variable has the similar meaning ( note, that for angles it is specified in radians ).
 out_step Grid spacing for the output grid. Normally, one wants to have this parameter smaller than fmatch.step, to have a smooth curve, without additional spline interpolation. As a rule of thumb we normally use fmatch.out_step which is approximately 5 times smaller than fmatch.step.
 step grid spacing for the spline, which represents the interaction. This parameter should not be too big, otherwise you might lose some features of the interaction potential, and not too small either, otherwise you will have unsampled bins which result in an illdefined equation system and NaNs in the output.
 inverse Contains all information relevant to iterative process
 do_potential Update cycle for the potential update. 1 means update, 0 don't update. 1 1 0 means update 2 iterations, then don't one iteration update, then repeat. (default 1)
 espresso Espresso specific options for this interations
 espresso.index1 Index list of type1  Name of the Tcl variable containing all index1 particles that is contained in the espresso blockfile.
 espresso.index2 Index list of type2  Name of the Tcl variable containing all index1 particles that is contained in the espresso blockfile.
 espresso.table Name of file for tabulated potential of this interaction. This fill will be created from the internal tabulated potential format in every step. Note, though, that the original espresso blockfile needs to contain the name of that table as the tabulated interaction (see tutorial methanol ibi_espresso for details).
 gromacs Gromacs specific options for this interations
 gromacs.table Name of file for tabulated potential of this interaction. This fill will be created from the internal tabulated potential format in every step.
 imc ection containing inverse monte carlo specific options.
 imc.group Group of interaction. Crosscorrelations of all members of a group are taken into account for calculating the update. If no cross correlations should be calculated, interactions have to be put into different groups.
 optimizer
 optimizer.density Contains all options for the density calculation of the optimizer
 optimizer.density.axis Axis along which the density is calculated (default x)
 optimizer.density.max Upper bound of interval in which density calculation is performed.
 optimizer.density.min Lower bound of interval in which density calculation is performed.
 optimizer.density.molname The molname of this interaction (default *)
 optimizer.density.step Step size of interval in which density calculation is performed.
 optimizer.density.target Filename of the target denstiy distribution in the maindir
 optimizer.function Functional form of the interaction, using parameters in here
 optimizer.functionfile If the function is very complicated it can be defined in this files, which is used as an header
 optimizer.mapping option related to mapping changes
 optimizer.mapping.change Does the mapping change in optimization: yes/no (default no)
 optimizer.mapping.output Output file name for mapping (default no)
 optimizer.mapping.template template for the mapping optimization
 optimizer.parameters Parameters to be fitted by the optimizer for this interaction. Note that the parameter names are global
 optimizer.pressure Contains all options for the pressure calculation of the optimizer
 optimizer.pressure.undef Pressure to use if pressure from the simulation was nan (use a big number)
 optimizer.rdf Contains all options for the rdf calculation of the optimizer
 optimizer.rdf.target Filename of the target rdf in the maindir
 optimizer.rdf.weight Weighting function for calculating the convergency of the rdf
 optimizer.rdf.weightfile File with the weighting function definition calculating the rdf
 optimizer.targets Targets to be fitted by the optimizer (default rdf)
 optimizer.target_weights Weight of the targets, amount has to be the same as of targets (default 1)
 particle_dens particle density of this species (for wjk pressure correction)
 post_add Additional post processing of U after dU added to potential. This is a list of scripts separated by spaces which are called. See section on iterative framework for details.
 post_add_options Contains all options of post add scripts
 post_add_options.convergence
 post_add_options.convergence.weight weight factors for the convergence of this interaction, should be a list of same length as inverse.post_add_options.convergence.what (default 1)
 post_add_options.convergence.what list from what to calc the convergence: dist pot, .. (default dist)
 post_add_options.copyback Contains all options of the postadd copyback sripts
 post_add_options.copyback.filelist File to be copied to back to maindir
 post_add_options.overwrite Contains all options of the overwrite postadd scripts
 post_add_options.overwrite.do Cycle for overwrite postadd script (1 do, 0 do not) like do_potential. (default 1)
 post_add_options.plot Contains all options of the plot postadd scripts
 post_add_options.plot.fd file descriptor to use, make it unique if you want to plot multiple things (default 8)
 post_add_options.plot.gnuplot_opts extra options to give to gnuplot_bin like persist or geometry
 post_add_options.plot.kill kill all processes with that name before ploting (e.g. gnuplot_x11), this is more reliable than using named pipes
 post_add_options.plot.script plot script to give to gnuplot
 post_update Additional postprocessing of dU before added to potential. This is a list of scripts separated by spaces which are called. See section on iterative framework for details.
 post_update_options Contains all options of post update scripts
 post_update_options.extrapolate
 post_update_options.extrapolate.points Number of point to calculate the average from for the extrapolation (default 5)
 post_update_options.kbibi Contains all options of the KirkwoodBuff corrections scripts (default no)
 post_update_options.kbibi.do Update cycle for the KirkwoodBuff correction (1 do, 0 do not). To do the correction every third step specify "0 0 1", similar to do_potential (default 1)
 post_update_options.kbibi.factor scaling factor for the ramp correction
 post_update_options.kbibi.kbint_with_errors calculate errors on the KirkwoodBuff integral: yes/no (default no)
 post_update_options.kbibi.r_ramp cutoff of the ramp
 post_update_options.kbibi.start Where to start averaging the KirkwoodBuff integral for the ramp
 post_update_options.kbibi.stop Where to stop averaging the KirkwoodBuff integral for the ramp
 post_update_options.kbibi.type Type of correction to be done: ramp/integral (default ramp)
 post_update_options.pressure Contains all options of the pressure correction scripts
 post_update_options.pressure.do Update cycle for the pressure correction (1 do, 0 do not). To do pressure correction every third step specify "0 0 1", similar to do_potential (default 1)
 post_update_options.pressure.simple Contains all options of the simple pressure correction
 post_update_options.pressure.simple.scale slope of the simple pressure correction
 post_update_options.pressure.type Pressure correction type, can be simple or wjk (default simple)
 post_update_options.pressure.wjk Contains all options of the wjk pressure correction
 post_update_options.pressure.wjk.scale extra scaling factor of pressure wjk correction (default 1.0)
 post_update_options.scale scale factor for the update (default 1.0)
 post_update_options.smooth Contains all options of the post_update smooth script
 post_update_options.smooth.iterations number of triangular smooth to be performed (default 1)
 post_update_options.splinesmooth Contains all options of the post_update spline smooth script
 post_update_options.splinesmooth.step grid spacing for spline fit when doing spline smoothing
 p_target pressure contribution of this interaction
 target target distribution (e.g. rdf) which is tried to match during iterations to match
 tf Contains all information relevant to thermoforce iteration
 tf.cg_prefactor Prefactor for the thermoforce will be linear interpolated with tf.prefactor
 tf.molname Molecule name of this interaction used in gromacs topology (default *)
 tf.prefactor Prefactor for the thermoforce (f=prefactor csg_defaults.xml.t2t Makefile Makefile.incl Makefile.XMLS xml2t2t.sh grad density)
 tf.spline_end End of the spline used to smooth the density
 tf.spline_start Start of the spline used to smooth the density
 tf.spline_step Grid of the spline used to smooth the density
 max Upper bound of interval for potential table in which calculations are performed. Should be set based on reference distributions.
 min Lower bound of interval for potential table in which calculations are performed. Should be set based on reference distributions.
 name Name of the interaction. The name can be arbitrary but should be unique. For bonded interactions, this should match the name specified in the mapping file.
 step Step size of interval for potential table in which calculations are performed. If step site is too small, lots of statistics is needed ( long runs ). If it's too big, features in the distribtuion/potentials might get lost.
 type1 Bead type 1 of nonbonded interaction.
 type2 Bead type 2 of nonbonded interaction.
