Section containing the all coarse-graining options The following table contains the input options for CSG,

Property Name | Default Value | Description
--- | --- | ---
fmatch |  | Force matching options
fmatch.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.
fmatch.dist | 1e-5 | Accuracy for evaluating the difference in bead positions. Default is 1e-5
fmatch.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. Coarse-grained force-field, which one gets on the output is averaged over those blocks.
inverse |  | general options for inverse script
inverse.cleanlist |  | these files are removed after each iteration
inverse.convergence_check |  |
inverse.convergence_check.limit | 0 | lower convergency limit to stop
inverse.convergence_check.type | none | type of convergence check to do
inverse.dlpoly |  | general dlpoly specific options
inverse.dlpoly.command | DLPOLY.Z | command to run dlpoly (name or absolute path or ‘mpirun dlpoly’ or such)
inverse.dlpoly.topol | .dlpf | Name of dlpoly topology file
inverse.dlpoly.traj | .dlph | Name of the output dlpoly trajectory file
inverse.dlpoly.checkpoint | REVIVE REVCON | Names of the dlpoly checkpoint files
inverse.dlpoly.table_end |  | dlpoly internal grid end point for tabulated non-bonded potentials (applied to all non-bonded)
inverse.dlpoly.table_grid |  | dlpoly internal grid number for tabulated non-bonded potentials (applied to all non-bonded)
inverse.dlpoly.bonds |  | dlpoly specs for tabulated bonded potentials (applied to all bonds)
inverse.dlpoly.bonds.table_end |  | dlpoly internal grid end point for tabulated potentials
inverse.dlpoly.bonds.table_grid |  | dlpoly internal grid number for tabulated potentials
inverse.dlpoly.angles |  | dlpoly specs for tabulated bonded potentials (applied to all angles)
inverse.dlpoly.angles.table_grid |  | dlpoly internal grid number for tabulated potentials
inverse.dlpoly.dihedrals |  | dlpoly specs for tabulated bonded potentials (applied to all dihedrals)
inverse.dlpoly.dihedrals.table_grid |  | dlpoly internal grid number for tabulated potentials
inverse.espresso |  |
inverse.espresso.command | python3 | Command to run espresso (name or absolute path or mpirun espresso..)
inverse.espresso.opts | ${script} | option to be given to espresso program, use ${script} in there
inverse.espresso.first_frame | 0 | trash the given number of frames at the beginning of trajectory
inverse.espresso.table_bins |  | espresso internal grid for tabulated potentials
inverse.espresso.traj |  | Name of the output Espresso trajectory file
inverse.espressopp |  |
inverse.espressopp.command | python3 | Command to run espresso (name or absolute path or mpirun espresso..)
inverse.espressopp.opts | ${script} | option to be given to espresso program, use ${script} in there
inverse.espressopp.first_frame | 0 | trash the given number of frames at the beginning of trajectory
inverse.filelist |  | these files are copied to each iteration step
inverse.gnuplot |  |
inverse.gnuplot.bin | gnuplot | gnuplot binary to use
inverse.gromacs |  | gromacs specific options
inverse.gromacs.conf | conf.gro | Name of the coordinate file read by grompp
inverse.gromacs.conf_out | confout.gro | Name of the original outcome coordinate written by mdrun
inverse.gromacs.density |  |
inverse.gromacs.density.block_length |  | Length of the block for the error analysis
inverse.gromacs.density.with_errors | no | calculate error on the density: yes/no
inverse.gromacs.equi_time | 0 | begin analysis after this time when using gromacs (max of this and first_frame is used)
inverse.gromacs.first_frame | 0 | trash the given number of frames at the beginning of trajectory (max of this and first_frame is used)
inverse.gromacs.g_energy |  |
inverse.gromacs.g_energy.bin | /usr/bin/gmx_d energy | Name (or absolute path) of the g_energy binary
inverse.gromacs.g_energy.opts |  | Additional options to Gromacs g_energy (e.g. -P 1)
inverse.gromacs.g_energy.pressure |  | options for pressure calculation using g_energy
inverse.gromacs.g_energy.pressure.allow_nan | no | is nan an allowed result: yes/no
inverse.gromacs.g_energy.topol |  | Gromacs binary topol (tpr) file to use by g_energy
inverse.gromacs.gmxrc |  | GMXRC to source at the startup
inverse.gromacs.grompp |  |
inverse.gromacs.grompp.bin | /usr/bin/gmx_d grompp | Name (or absolute path) of the grompp binary
inverse.gromacs.grompp.opts |  | Additional options to Gromacs grompp (e.g. -maxwarn 1)
inverse.gromacs.index | index.ndx | Gromacs grompp index file to used by grompp
inverse.gromacs.log |  | Separate log file for gromacs programs (useful with mdrun -v)
inverse.gromacs.mdp | grompp.mdp | Gromacs mdp file to be used by grompp
inverse.gromacs.mdrun |  |
inverse.gromacs.mdrun.checkpoint | state.cpt | Name of the checkpint to use in case of restarted simulation
inverse.gromacs.mdrun.command | /usr/bin/gmx_d mdrun | Command to run mdrun (name or absolute path or mpirun mdrun..)
inverse.gromacs.mdrun.multidir |  | List of directories for multidir simulations
inverse.gromacs.mdrun.opts |  | Additional options to Gromacs mdrun (e.g. -nosum)
inverse.gromacs.pot_max | 1000000 | cut the potential at this value (gromacs bug)
inverse.gromacs.pre_simulation | no | A pre simulation (e.g. minimization / equilibration ) is a simulation with a different mdp/topol/index
inverse.gromacs.pre_simulation.index |  | Gromacs grompp index file to used by grompp in the pre simulation
inverse.gromacs.pre_simulation.mdp |  | Gromacs mdp file to be used by grompp in the pre simulation
inverse.gromacs.pre_simulation.topol_in |  | Gromacs text topol (top) file to use by grompp in the pre simulation
inverse.gromacs.ref |  | Options for the case that calculation of reference system is needed
inverse.gromacs.ref.equi_time | 0 | begin analysis after this time when using gromacs (max of this and first_frame is used)
inverse.gromacs.ref.first_frame | 0 | trash the given number of frames at the beginning of trajectory (max of this and first_frame is used)
inverse.gromacs.ref.mapping |  | Mapping to apply on the coarse-grained topology, use autogenerated ones (cg.inverse.optimizer.mapping.output) and given ones (map other components)
inverse.gromacs.ref.rdf |  | Contains options for Reference rdf calculation
inverse.gromacs.ref.rdf.opts |  | Extra options to give to csg_stat (e.g. –nframes 100)
inverse.gromacs.ref.topol |  | Reference binary topology(global or local path)
inverse.gromacs.ref.traj |  | Reference trajectory(global or local path)
inverse.gromacs.rdf |  |
inverse.gromacs.rdf.block_length |  | Length of the block for the error analysis
inverse.gromacs.rdf.map |  | Space separated list of special mapping file(s) for rdf calculations needed for bonded interactions
inverse.gromacs.rdf.with_errors | no | calculate error on the rdf: yes/no
inverse.gromacs.table_bins | 0.002 | grid for gromacs xvg table
inverse.gromacs.table_end |  | extend the gromacs xvg tables to this value
inverse.gromacs.temp_check | yes | check kBT against t_ref in mdp file: yes/no
inverse.gromacs.topol_in | topol.top | Gromacs text topology (top) file read by grompp
inverse.gromacs.topol | topol.tpr | Gromacs binary topology (tpr) file to be written by grompp and used for the simlation
inverse.gromacs.traj | traj.xtc | Gromacs trajectory file to use
inverse.gromacs.trjcat |  |
inverse.gromacs.trjcat.bin | /usr/bin/gmx_d trjcat | Name (or absolute path) of the trjcat binary
inverse.hoomd-blue |  |
inverse.hoomd-blue.command | hoomd | Command to run hoomd-blue (name or absolute path or mpirun ..)
inverse.hoomd-blue.opts | ${script} | option to be given to hoomd-blue program, use ${script} in there
inverse.imc |  | general imc specific options
inverse.imc.default_reg | 0 | default magnitude for regularization parameter if not given for the group explicitly, default =0
inverse.lammps |  | general lammps specific options
inverse.lammps.command | lmp | command to run lammps (name or absolute path or mpirun lammps..)
inverse.lammps.script |  | lammps script to run
inverse.lammps.opts | -in ${script} | option to be given to lammps program, use ${script} in there
inverse.lammps.traj |  | trajectory file to be created by lammps, use a format like xyz, which can be read by csg_stat
inverse.lammps.pressure_file |  | pressure file generated by lammps, use “fix print” in lammps input (e.g., “fix pressure all print 50 “${mypress}” file lammps.pressure screen no title “LAMMPS_PRESSURE” “ ; pressure_file would be lammps.pressure in this example). The title can be anything as VOTCA skips over this line as a header when parsing
inverse.sim_prog |  | options, which apply to all simulation programs
inverse.sim_prog.command |  | Command to run for the simulation (name or absolute path or mpirun XXX ..)
inverse.sim_prog.conf |  | Name of the coordinate file read by the simulation program (if needed)
inverse.sim_prog.conf_out |  | Name of the original outcome coordinate written by simulation program (if any)
inverse.sim_prog.equi_time | 0 | begin analysis after this time (max of this and first_frame is used)
inverse.sim_prog.density |  |
inverse.sim_prog.density.block_length |  | Length of the block for the error analysis
inverse.sim_prog.density.with_errors | no | calculate error on the density: yes/no
inverse.sim_prog.first_frame | 0 | trash the given number of frames at the beginning of trajectory (max of this and first_frame is used)
inverse.sim_prog.imc |  |
inverse.sim_prog.imc.topol |  | Special topology file to be used for csg_stat used in imc
inverse.sim_prog.imc.traj |  | Special trajectory file to be used for csg_stat used in imc
inverse.sim_prog.re |  |
inverse.sim_prog.re.topol |  | Special topology file to be used for csg_reupdate
inverse.sim_prog.re.traj |  | Special trajectory file to be used for csg_reupdate
inverse.sim_prog.rdf |  |
inverse.sim_prog.rdf.block_length |  | Length of the block for the error analysis
inverse.sim_prog.rdf.map |  | Space separated list of special mapping file(s) for rdf calculations needed for bonded interactions
inverse.sim_prog.rdf.topol |  | Special topology file to be used for csg_stat
inverse.sim_prog.rdf.traj |  | Special trajectory file to be used for csg_stat
inverse.sim_prog.rdf.with_errors | n | calculate error on the rdf: yes/no
inverse.sim_prog.topol |  | General topology file to be use if no special one is specified
inverse.sim_prog.traj |  | trajectory file to be created by the simulation program
inverse.sim_prog.script |  | simulation script to run (if any)
inverse.sim_prog.opts |  | option to be given to simulation program, use ${script} in there
inverse.re |  | general options for realtive entropy method
inverse.re.csg_reupdate |  |
inverse.re.csg_reupdate.opts |  | options for the csg_reupdate command
inverse.average |  |
inverse.average.steps | 1 | number of steps to be used for average computation. For relative entropy method, these many last iteration steps are used to compute average CG potentials or parameters or both.
inverse.initial_configuration | maindir | what initial configuration to use in every step: maindir/laststep/nowhere.
inverse.iterations_max |  | do the given number of iterations (-1=inf, 0=only step_000)
inverse.kBT |  | kBT in KJ/mol (i.e. XXX K * 0.00831451)
inverse.log_file | inverse.log | name of the log file
inverse.map |  | Special mapping file(s) for rdf calculations needed for bonded interactions
inverse.method |  | method to be performed: ibi/iie/imc/ft/optimizer
inverse.iie |  | general options for the IIE schemes (hncgn/ihnc/hncn/pygn/ipy/pyn)
inverse.iie.initial_guess |  | Settings for the initial guess
inverse.iie.initial_guess.method | ie | Method for the initial potential guess: table/bi/ie
inverse.iie.initial_guess.closure |  | OZ equation closure in case of method=ie: hnc/py
inverse.iie.initial_guess.ignore_intramolecular_correlation | false | If true, the initial guess will ignore the presence of intramolecular correlation in the CG molecule.
inverse.iie.method | gauss-newton | Update method to use: gauss-newton/newton/newton-mod. For example closure=hnc + method=gauss-newton will result in the HNCGN method. newton_mod is a modified newton scheme that results in an IBI like expression e.g. IHNC.
inverse.iie.closure | hnc | OZ equation closure for the IIE update: hnc/py
inverse.iie.ignore_intramolecular_correlation | false | If true, the IIE updates (not the initial guess) will ignore the presence of intramolecular correlation in the CG molecule.
inverse.iie.cut_off |  | Cut-off used for non-bonded potenitals in MD. Potential will be set to zero beyond this point.
inverse.iie.g_extrap_factor | 1.0 | Lenght factor by which RDF will be extrapolated
inverse.iie.cut_jacobian | true | Wether to cut the Jacobian before multiplying with Δg. Only for Newton methods
inverse.iie.densities |  | List of densities of the beads, sorted by bead name. TODO: replace by automatic calculation.
inverse.iie.n_intra |  | List of n_intra, the number of equal beads, sorted by bead name. TODO: replace by automatic calculation.
inverse.iie.pressure_constraint | none | Apply pressure constraint. Only for hncgn/pygn
inverse.iie.extrap_near_core | power | Method for extrapolation in and close to core region. Valid values are: power (default), constant, none
inverse.iie.fix_near_cut_off | full-deriv | Method for fixing discontinuity at end of potential. Valid values are: full-deriv (default), none
inverse.iie.verbose | true | Print some info and dump compressed numpy arrays. Valid values are: true (default), false
inverse.optimizer |  |
inverse.optimizer.cma |  | general options for the cma optimizer
inverse.optimizer.cma.eps |  | standard epsilon, in which the best solution is searched
inverse.optimizer.type |  | Type of optimizer to be used
inverse.program | gromacs | simulation package to be used (gromacs/espresso/lammps)
inverse.restart_file | restart_points.log | Name of the restart file in case a step has to be resumed
inverse.dist_min | 1e-10 | minimal value for the rdf to consider for initial guess of the potential)
inverse.scriptpath |  | list of directories for user scripts (e.g. $PWD) separated by a colon (like PATH)
inverse.simulation |  | simulation options
inverse.simulation.background | no | tells csg_inverse that simulation was send to the backgroud
inverse.simulation.tasks | auto | number of threads to use for csg_stat
inverse.scale |  | update scaling factor for the relative entropy update
nbsearch | grid | Grid search algorithm, simple (N square search) or grid
bonded |  | Interaction specific option for bonded interactions, see the cg.non-bonded section for all options
bonded.dlpoly |  |
bonded.dlpoly.header |  | Header of the interaction in dlpoly TABBND or TABANG file. The header should be a unique set of the interaction-site names, and these should match the corresponding names specified in the mapping file.
bonded.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.
bonded.periodic | 0 | set to 1 when calculating bond dihedral potentials with csg_fmatch -> enforces periodicity of potential. (default is 0)
non-bonded |  | Interaction specific option for non-bonded interactions
non-bonded.dlpoly |  |
non-bonded.dlpoly.header |  | Header of the interaction in dlpoly TABLE file. The header should be a unique pair of the interaction-site names, and these should match the corresponding names specified in the mapping file.
non-bonded.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.
non-bonded.type1 |  | Bead type 1 of non-bonded interaction.
non-bonded.type2 |  | Bead type 2 of non-bonded interaction.
non-bonded.bondtype |  | Internal alias for “non-bonded” or “bonded”, set automatically
non-bonded.min |  | Lower bound of interval for potential table in which calculations are performed. Should be set based on reference distributions.
non-bonded.max |  | Upper bound of interval for potential table in which calculations are performed. Should be set based on reference distributions.
non-bonded.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.
non-bonded.fmatch |  | Force matching options
non-bonded.fmatch.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 non-bonded 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 ).
non-bonded.fmatch.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 non-bonded interactions it’s the cut-off of the interaction.
non-bonded.fmatch.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 ill-defined equation system and NaNs in the output.
non-bonded.fmatch.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.
non-bonded.re |  | Relative entropy options
non-bonded.re.function |  | Functional form for the potential. Available functional forms: lj126 (Lennard-Jones 12-6), ljg (Lennard-Jones 12-6 plus Gaussian), and cbspl (uniform cubic B-splines).
non-bonded.re.cbspl |  | options specific to cbspl function form

non-bonded.re.cbspl.nknots

Number of knot values to be used for the cbspl functional
form. Uniform grid size of the CBSPL depends on this parameter;
for fixed potential range more the nknots smaller the
grid spacing. Make sure grid spacing is sufficiently large
and enough CG simulation steps are performed such that
the bins at distance greater than the minimum distance
are sampled sufficiently otherwise ill-defined system
of equation would give NaNs in the output.

non-bonded.inverse |  | Contains all information relevant to iterative process
non-bonded.inverse.target |  | target distribution (e.g. rdf) which is tried to match during iterations to match
non-bonded.inverse.p_target |  | pressure contribution of this interaction
non-bonded.inverse.particle_dens |  | particle density of this species (for wjk pressure correction)
non-bonded.inverse.do_potential | 1 | 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.
non-bonded.inverse.espresso |  | Espresso specific options for this interations
non-bonded.inverse.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 script needs to contain the name of that table as the tabulated interaction (see tutorial methanol ibi_espresso for details).
non-bonded.inverse.espressopp |  | Espresso++ specific options for this interations
non-bonded.inverse.hoomd-blue |  | HOOMD-blue specific options for this interations
non-bonded.inverse.gromacs |  | Gromacs specific options for this interations
non-bonded.inverse.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.
non-bonded.inverse.sim_prog |  | interaction specific options, which apply to all simulation programs
non-bonded.inverse.sim_prog.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 simulation script needs to contain the name of that table as the tabulated interaction (see tutorial methanol ibi_espresso for details).
non-bonded.inverse.sim_prog.table_begin |  | Start of the tabulated potential of this interaction. (Automatic for gromacs)
non-bonded.inverse.sim_prog.table_end |  | End of the tabulated potential of this interaction. (Automatic for gromacs)
non-bonded.inverse.sim_prog.table_left_extrapolation |  | Extrapolation function to use on the left. Default: exponential(non-bonded), linear (bonded), Options: constant linear quadratic exponential sasha
non-bonded.inverse.sim_prog.table_right_extrapolation |  | Extrapolation function to use on the right. Default: constant(non-bonded), linear (bonded), Options: constant linear quadratic exponential sasha
non-bonded.inverse.sim_prog.table_bins |  | Binszie of the tabulated potential of this interaction. (gromacs uses a non interaction specific option)
non-bonded.inverse.imc |  | section containing inverse monte carlo specific options.
non-bonded.inverse.imc.group |  | Group of interaction. Cross-correlations 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. Group ‘none’ is completely ignored and update_potential needs to be zero for the respective interactions.
non-bonded.inverse.lammps |  | lammps specific options for this interations
non-bonded.inverse.lammps.scale | 1 | x-axis scaling factor for the potential output, can be used to convert VOTCA units, nm, to other units, e.g. angstroms
non-bonded.inverse.lammps.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 lammps script needs to contain the name of that table as the tabulated interaction and the interaction is stored in the VOTCA section of the file..
non-bonded.inverse.lammps.y_scale | 1 | y-axis scaling factor for the potential output, can be used to convert VOTCA units, kJ/mol, to other units, e.g. kcal/mol
non-bonded.inverse.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.
non-bonded.inverse.post_add_options |  | Contains all options of post add scripts
non-bonded.inverse.post_add_options.compress |  | Contains all options of the postadd compress sripts
non-bonded.inverse.post_add_options.compress.filelist |  | Files to be compressed
non-bonded.inverse.post_add_options.compress.program_opts | -9 | Option to give to the compression command
non-bonded.inverse.post_add_options.compress.program | gzip | Compression command to run
non-bonded.inverse.post_add_options.convergence |  |
non-bonded.inverse.post_add_options.convergence.weight | 1 | weight factors for the convergence of this interaction, should be a list of same length as inverse.post_add_options.convergence.what
non-bonded.inverse.post_add_options.convergence.what | dist | list from what to calc the convergence: dist pot, ..
non-bonded.inverse.post_add_options.convergence.base | tgt | what base values to be used to compute convergene error: tgt, cur, ..
non-bonded.inverse.post_add_options.convergence.norm | 1 | which norm to use to compute error: 1 first norm, 2 second norm
non-bonded.inverse.post_add_options.copyback |  | Contains all options of the postadd copyback sripts
non-bonded.inverse.post_add_options.copyback.filelist |  | File to be copied to back to maindir
non-bonded.inverse.post_add_options.overwrite |  | Contains all options of the overwrite postadd scripts
non-bonded.inverse.post_add_options.overwrite.do | 1 | Cycle for overwrite postadd script (1 do, 0 do not) like do_potential.
non-bonded.inverse.post_add_options.plot |  | Contains all options of the plot postadd scripts
non-bonded.inverse.post_add_options.plot.fd | 8 | file descriptor to use, make it unique if you want to plot multiple things
non-bonded.inverse.post_add_options.plot.gnuplot_opts |  | extra options to give to gnuplot_bin like -persist or -geometry
non-bonded.inverse.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
non-bonded.inverse.post_add_options.plot.script |  | plot script to give to gnuplot
non-bonded.inverse.post_add_options.average |  |
non-bonded.inverse.post_add_options.average.what |  | list for which averages of last few steps are to computed: param, pot, … For relative entropy method, specify param before pot.
non-bonded.inverse.post_update |  | Additional post-processing 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.
non-bonded.inverse.post_update_options |  | Contains all options of post update scripts
non-bonded.inverse.post_update_options.cibi |  | Contains all options of the Kirkwood-Buff integral corrections scripts
non-bonded.inverse.post_update_options.cibi.do | 1 | Update cycle for the Kirkwood-Buff integral correction (1 do, 0 do not). To do the correction every third step specify “0 0 1”, similar to do_potential
non-bonded.inverse.post_update_options.cibi.kbint_with_errors | no | calculate errors on the Kirkwood-Buff integral: yes/no
non-bonded.inverse.post_update_options.extrapolate |  |
non-bonded.inverse.post_update_options.extrapolate.points | 5 | Number of point to calculate the average from for the extrapolation
non-bonded.inverse.post_update_options.ibi |  | Contains all options of the IBI post-update script
non-bonded.inverse.post_update_options.ibi.do | 1 | Update cycle for the IBI post-update (1 do, 0 do not). To do the post-update every third step specify “0 0 1”, similar to do_potential
non-bonded.inverse.post_update_options.kbibi |  | Contains all options of the Kirkwood-Buff ramp corrections scripts
non-bonded.inverse.post_update_options.kbibi.do | 1 | Update cycle for the Kirkwood-Buff ramp correction (1 do, 0 do not). To do the correction every third step specify “0 0 1”, similar to do_potential
non-bonded.inverse.post_update_options.kbibi.factor |  | scaling factor for the ramp correction
non-bonded.inverse.post_update_options.kbibi.kbint_with_errors | no | calculate errors on the Kirkwood-Buff integral: yes/no
non-bonded.inverse.post_update_options.kbibi.r_ramp |  | cutoff of the ramp
non-bonded.inverse.post_update_options.kbibi.start |  | Where to start averaging the Kirkwood-Buff integral for the ramp
non-bonded.inverse.post_update_options.kbibi.stop |  | Where to stop averaging the Kirkwood-Buff integral for the ramp
non-bonded.inverse.post_update_options.lj |  | Contains all options of the Lennard-Jones potential update
non-bonded.inverse.post_update_options.lj.c6 |  | The c6 value for the extra LJ potential
non-bonded.inverse.post_update_options.lj.c12 |  | The c12 value for the extra LJ potential
non-bonded.inverse.post_update_options.pressure |  | Contains all options of the pressure correction scripts
non-bonded.inverse.post_update_options.pressure.do | 1 | 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
non-bonded.inverse.post_update_options.pressure.simple |  | Contains all options of the simple pressure correction
non-bonded.inverse.post_update_options.pressure.simple.max_A | 0.1 | maximum prefactor in units of kBT
non-bonded.inverse.post_update_options.pressure.simple.scale |  | slope of the simple pressure correction
non-bonded.inverse.post_update_options.pressure.ptype |  | Generic Pressure correction options
non-bonded.inverse.post_update_options.pressure.ptype.max_A |  | maximum prefactor in units of kBT
non-bonded.inverse.post_update_options.pressure.ptype.scale |  | slope of the pressure correction
non-bonded.inverse.post_update_options.pressure.type | simple | Pressure correction type, can be simple or wjk
non-bonded.inverse.post_update_options.pressure.wjk |  | Contains all options of the wjk pressure correction
non-bonded.inverse.post_update_options.pressure.wjk.max_A | 0.1 | maximum prefactor in units of kBT
non-bonded.inverse.post_update_options.pressure.wjk.scale | 1.0 | extra scaling factor of pressure wjk correction
non-bonded.inverse.post_update_options.scale | 1.0 | scale factor for the update
non-bonded.inverse.post_update_options.smooth |  | Contains all options of the post_update smooth script
non-bonded.inverse.post_update_options.smooth.iterations | 1 | number of triangular smooth to be performed
non-bonded.inverse.post_update_options.splinesmooth |  | Contains all options of the post_update spline smooth script
non-bonded.inverse.post_update_options.splinesmooth.step |  | grid spacing for spline fit when doing spline smoothing
non-bonded.inverse.optimizer |  |
non-bonded.inverse.optimizer.density |  | Contains all options for the density calculation of the optimizer
non-bonded.inverse.optimizer.density.axis | x | Axis along which the density is calculated
non-bonded.inverse.optimizer.density.min |  | Lower bound of interval in which density calculation is performed.
non-bonded.inverse.optimizer.density.max |  | Upper bound of interval in which density calculation is performed.
non-bonded.inverse.optimizer.density.step |  | Step size of interval in which density calculation is performed.
non-bonded.inverse.optimizer.density.scale | 1.0 | Scaling factor for density

non-bonded.inverse.optimizer.density.molname

The molname of this interaction

non-bonded.inverse.optimizer.density.target |  | Filename of the target denstiy distribution in the maindir
non-bonded.inverse.optimizer.function |  | Functional form of the interaction, using parameters in here
non-bonded.inverse.optimizer.functionfile |  | If the function is very complicated it can be defined in this files, which is used as an header
non-bonded.inverse.optimizer.mapping |  | option related to mapping changes
non-bonded.inverse.optimizer.mapping.change | no | Does the mapping change in optimization: yes/no
non-bonded.inverse.optimizer.mapping.output | no | Output file name for mapping
non-bonded.inverse.optimizer.mapping.template |  | template for the mapping optimization
non-bonded.inverse.optimizer.parameters |  | Parameters to be fitted by the optimizer for this interaction. Note that the parameter names are global
non-bonded.inverse.optimizer.pressure |  | Contains all options for the pressure calculation of the optimizer
non-bonded.inverse.optimizer.pressure.undef |  | Pressure to use if pressure from the simulation was nan (use a big number)
non-bonded.inverse.optimizer.rdf |  | Contains all options for the rdf calculation of the optimizer
non-bonded.inverse.optimizer.rdf.target |  | Filename of the target rdf in the maindir
non-bonded.inverse.optimizer.rdf.weight |  | Weighting function for calculating the convergency of the rdf
non-bonded.inverse.optimizer.rdf.weightfile |  | File with the weighting function definition calculating the rdf
non-bonded.inverse.optimizer.targets | rdf | Targets to be fitted by the optimizer
non-bonded.inverse.optimizer.target_weights | 1 | Weight of the targets, amount has to be the same as of targets