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cgoptions

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  • cg Section containing the all coarse-graining options
    • bonded Interaction specific option for bonded interactions, see the cg.non-bonded 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. Coarse-grained force-field, 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 non-bonded 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 coarse-grained 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)
    • non-bonded Interaction specific option for non-bonded interactions
      • bondtype Internal alias for "non-bonded" 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 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 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. 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.
        • 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 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
        • 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 Kirkwood-Buff corrections scripts (default no)
        • post_update_options.kbibi.do Update cycle for the Kirkwood-Buff 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 Kirkwood-Buff 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 Kirkwood-Buff integral for the ramp
        • post_update_options.kbibi.stop Where to stop averaging the Kirkwood-Buff 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 non-bonded interaction.
      • type2 Bead type 2 of non-bonded interaction.
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