- bondtype Internal alias for non-bonded and 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 non-bonded interactions it's the cut-off 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 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 ).
- 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 ill-defined 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 update, then repeat.
- espresso This section contains espresso specific options in case espresso is used as simulation program.
- index1 Index list of type1 -- Name of the Tcl variable containing all index1 particles that is contained in the espresso blockfile.
- index2 Index list of type2 -- Name of the Tcl variable containing all index2 particles that is contained in the espresso blockfile.
- table Name of file for tabulated potential of this interaction. This file will be created from the internal tabulated potential format for every run. 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 This section contains gromacs specific options in case gromacs is used as simulation program.
- grp1 Name of energy group of bead type1 using in the g_rdf index file.
- grp2 Name of energy group of bead type2 using in the g_rdf index file.
- table Name of file for tabulated potential of this interaction. This fill will be created from the internal tabulated potential format for every run.
- imc Section containing inverse monte carlo specific options.
- 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.
- 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 This section contains all options for post add scripts.
- convergence
- weight weight factors for the convergence of the interaction, should be a list of same length as inverse.post_add_options.convergence.what (default 1)
- what list for what to calc the convergence: dist pot, .. (default dist)
- copyback
- filelist list of files to copy to the main dir
- overwrite Contains all options of the overwrite postadd scripts
- do pattern for overwrite postadd script (1 do, 0 do not).
- plot
- fd file descriptor to use (default 8), make it unique if you want to plot multiple things
- gnuplot_bin gnuplot binary to use (default gnuplot)
- gnuplot_opts extra options to give to gnuplot_bin (e.g. -persist, if one uses kill)
- kill kill all processes with that name before ploting (e.g. gnuplot_x11), this is more reliable than using multiplot
- script plot script to give to gnuplot
- 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.
- post_update_options Contains all options of post update scripts
- pressure Contains all options of the pressure correction scripts
- do pattern for pressure correction (1 do, 0 do not). To do pressure correction every third step specify "0 0 1", similar to inverse.do_update
- simple Contains all options of the simple pressure correction script
- simple.scale slope of the simple pressure correction
- type Pressure correction algoritm, can be simple or wjk
- wjk Contains all options of the wjk pressure correction script
- wjk.scale extra scaling factor of pressure correction
- scale scale factor for the update
- smooth Contains all options of the smooth script
- iterations number of iterations for triangular smooth
- splinesmooth Contains all options of the spline smooth script
- step grid spacing for spline fit when doing spline smoothing
- p_target partial pressure of this species
- target target distribution (e.g. rdf) which is tried to match during iterations to match
- 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.
- tf Contains all information relevant to thermoforce iteration
- cg_prefactor Second Prefactor for the thermoforce will be linear interpolated with tf.prefactor
- molname Molecule name of this gropu used in gromacs topology
- prefactor Prefactor for the thermoforce (f=-prefactor cginteraction.tex cginteraction.xml.t2t cgoptions.tex Makefile Makefile.incl Makefile.orig Makefile.XMLS mapping.tex %.t2t xml2t2t.sh grad density)
- spline_end End of the spline used to smooth the density
- spline_start Start of the spline used to smooth the density
- spline_step Grid of the spline used to smooth the density
- type1 Only for non-bonded. Bead type 1 of non-bonded interaction.
- type2 Only for non-bonded. Bead type 2 of non-bonded interaction.
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