The main.tcl file provided in the examples directory
is a relatively complete script written using mbtools. It is
designed to run all of the examples provided but no more. No doubt
you will need to extend it for your own purposes.
Variables used by main.tcl
main.tcl expects the user to set various
parameters in a parameters.tcl file (eg simplebilayer.tcl). Some
of these parameters have defaults and generally don't need to be
worried about except for specific cases. In the following list
variables that have no default and therefore must be set in the
parameter file are noted with an asterisk.
- thermo [Langevin] The type of thermostat to be used. Set to "DPD" for a dpd thermostat. Any other value gives a langevin
- dpd_gamma Required if you set the thermo to "DPD"
- dpd_r_cut Required if you set the thermo to "DPD"
- warmup_temp [$systemtemp] The temperature at which the warmup is performed.The default behaviour is to use the system temperature
- warmsteps [100] Number of integrate steps per warmup cycle
- warmtimes [20] Number of calls to integrate over which the warmup occurs
- free_warmsteps [0] Warmup steps to be used for the warmup that occurs after particles are freed of any temporary constraints.
- free_warmtimes [0] Warmup times to be used for the warmup that occurs after particles are freed of any temporary constraints.
- npt [off] Whether to use the constant pressure barostat
- p_ext The pressure you want to simulate at. Required if npt is set to "on"
- piston_mass box mass. Required if npt is set to "on"
- gamma_0 Required if npt is "on". Usually set to 1 as for langevin gamma
- gamma_v Required if npt is "on". Box friction
- use_vmd [offline] vmd mode
- mgrid [8] The number of meshpoints per side for dividing the bilayer plane into a grid
- stray_cut_off [1000.0] Distance of the end tail bead from the bilayer midplane beyond which a lipid is deemed to have strayed from the membrane bulk.
- *systemtemp The temperature of the simulation during the main run
- *outputdir Directory for output
- *tabledir Directory where forcetables are kept
- *identa name for the simulation
- *topofilethe name of the file where the topology is written. Usually $ident.top
- *tablenames A list of forcetable names to be used
- *setbox_l Box dimensions
- *bonded_parms A complete list of the bonded interactions required
- *nb_interactions A complete list of the non-bonded interactions required
- *system_specs A list of system specifications (see docu for the ::mbtools::system_generation::setup_system command)
- *moltypes A list of molecule types (see docu for ::mbtools::system_generation)
- *warm_time_step timestep to be used during warmup integration
- *main_time_step timestep for the main integration run
- *verlet_skinskin used for verlet nesting list criterion
- *langevin_gammalangevin friction term
- *int_n_timesnumber of times to do main integration
- *int_stepsnumber of steps in each main integration
- *analysis_write_frequencyHow often to calculate the analysis
- *write_frequencyHow often to print out configurations
- vmdcommands a list of additional lines of commands to be written to the vmd_animation.script file