- cg Yeah Head option, which contains all coarse-graining options
- bonded Section for a bonded interaction. Most of the items in here are identical to items in cg.bonded, so they will be described in the same section.
- 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 new run
- convergence_check type of convergence check to do
- convergence_check_options options for the convergence check
- limit lower limit to stop
- name_glob files to check for number (default *.conv)
- 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..)
- debug debug Espresso (yes/no)
- exclusions Espresso stuff to exclude
- first_frame rash the given number of frames at the beginning of trajectory
- 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 cginteraction.tex cginteraction.xml.t2t cginteraction.xml.tex cgoptions.tex cgoptions.xml.t2t config.t2t Makefile Makefile.incl Makefile.orig Makefile.XMLS mapping.tex %.t2t 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..)
- rdf_command Espresso command to run when calculating the rdf (name or absolute path or mpirun espresso..)
- scriptdir overwrite ESPRESSO_SCRIPTS from environment with this dir
- success File to create if Espresso simulation was successfull
- table_bins grid for tabulated potentials
- table_end Espresso end of table
- traj Name of the output Espresso trajectory file
- filelist these files are copied for each new run
- 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 interaction cutoffs against rvdw in mdp file: yes/no (default yes)
- equi_time begin analysis after this time when using gromacs
- first_frame trash the given number of frames at the beginning of trajectory
- g_energy
- g_energy.bin Name (or absolute path) of the g_energy binary
- g_energy.opts Additional options to Gromacs g_rdf (e.g. -P 1)
- g_energy.topol Gromacs g_rdf topol file to use, default topol.tpr
- gmxrc GMXRC to source at the startup
- g_rdf
- g_rdf.bin Name (or absolute path) of the g_rdf binary
- g_rdf.index Gromacs g_rdf index file to use, default index.ndx
- g_rdf.opts Additional options for Gromacs g_rdf (e.g. -nopbc)
- g_rdf.topol Gromacs g_rdf topol file to use, default topol.tpr
- grompp
- grompp.bin Name (or absolute path) of the grompp binary
- grompp.index Gromacs grompp index file to use, default index.ndx
- grompp.opts Additional options to Gromacs grompp (e.g. -maxwarn 1)
- grompp.topol Text Gromacs toplogy file to use, default topol.top
- mdp Gromacs mdp fie to use, 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..)
- mdrun.opts Additional options to Gromacs mdrun (e.g. -nosum)
- pot_max cut the potential at this value (gromacs bug)
- rdf
- rdf.topol Gromacs topol file to be used for csg_stat default topol.tpr
- table_bins grid for table*.xvg !
- table_end extend the tables to this value
- temp_check check temperture against t_ref in mdp file: yes/no (default yes)
- topol binary Gromacs topology file to use, 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
- octave
- octave.bin Name (or absolute path) of the octave binary
- solver solver for solving a linear equation system, can be octave or 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 (300*0.00831451 gromacs units)
- log_file write log to this file
- method ibi: inverse boltzmann imc: inverse monte carlo
- program simulation package to be used
- restart_file Name of the restart file in case a step has to be resumed
- scriptdir directory for user scripts (e.g. $PWD)
- $sim_prog generic simulation program (e.g. GROMACS) options
- equi_time begin analysis after this time
- first_frame trash the given number of frames at the beginning of trajectory
- simulation simulation options
- background tell csg_inverse that simulation was send to the backgroud (default no)
- tasks number of tasks (0/auto = automatic detect on linux)
- nbsearch Grid search algorithm, simple (N square search) or grid (default is grid)
- non-bonded Section for a non-bonded interaction. Most of the items in here are identical to items in cg.bonded, so they will be described in the same section.
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