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
|