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10.1. PROGRAMS
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--filter arg list option values that match given criteria
--print arg (=. ) list option values that match given criteria
--file arg xml file to parse
--short short version of output
--with-path include path of node in output
10.1.12
csg_resample
Change grid and interval of any sort of table files. Mainly called internally by inverse script, can
also be used to manually prepare input files for coarse-grained simulations.
Allowed options:
--help produce this help message
--in arg table to read
--out arg table to write
--derivative arg table to write
--grid arg new grid spacing (min:step:max). If ’grid’ is specified only, interpolation is
performed.
--type arg (=akima) [cubic|akima|linear]. If option is not specified, the default type
’akima’ is assumed.
--fitgrid arg specify fit grid (min:step:max). If ’grid’ and ’fitgrid’ are specified, a fit is
performed.
--nocut Option for fitgrid: Normally, values out of fitgrid boundaries are cut off. If they
shouldn’t, choose --nocut.
--comment arg store a comment in the output table
--boundaries arg (natural|periodic|derivativezero) sets boundary conditions
10.1.13
csg_stat
Calculate all distributions (bonded and non-bonded) specified in options file. Optionally calculates
update matrix for invere Monte Carlo. This program is called inside the inverse scripts. Unlike
csg_boltzmann, big systems can be treated as well as non-bonded interactions can be evaluated.
Allowed options:
-h [ --help ] produce this help message
--top arg atomistic topology file
Mapping options:
--cg arg [OPTIONAL] coarse graining mapping definitions (xml-file). If no file is given,
program acts on original trajectory
Specific options:
--options arg options file for coarse graining
--do-imc write out Inverse Monte Carlo data
--write-every arg write after every block of this length, if --blocking is set, the averages
are cleared after every output
--do-blocks write output for blocking analysis
Threading options:
--nt arg (=1) number of threads
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames