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

python2

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 (0=inf)

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

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.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