term¶
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
Specify a termination condition for a PB-(S)AM Brownian dynamics trajectory. The syntax is:
term {type} {options}
where the options
are determined by the type
as follows:
contact {file}
Termination based on molecular contact conditions.
file
is a string for the contact file filename. The contact file has a list formatted as follows:moltype1 at1 moltype2 at2 dist
wheremoltype1
andmoltype2
are indices of the molecular types,at1
is the index of an atom from the first molecular type,at2
is the index of an atom from the second molecular type, anddist
is the maximum distance between the two atoms that defines the contact.pad
is distance criterion that will be checked in the case that the true atom contact distance may not be fulfilled.Note
Sometimes these distances cannot be reached due to the assumption in this model that the molecule is spherical. If this is the case, the atom positions are transformed to the molecule surface and surface points are compared to the pad distance.
{pos} {val} {molecule}
Specify a position termination condition for a given molecule. where
pos
is one of the following options:x<=, x>=, y<=, y>=, z<=, z>=, r<=, r>=
.val
is the value along the given axis to check against.molecule
is the molecule index (1 based) according to the order of molecules listed in theREAD
section that this condition applies to. This command can be understood as: “Terminate the simulation when moleculemolecule
fulfills the conditionpos
val
”.Todo
Add a constant keyword (e.g., like
position
) before the{pos}
argument ofterm
. Documented in https://github.com/Electrostatics/apbs/issues/503time {val}
- Specify a time termination condition where
val
is a floating point number for the trajectory time limit (in picoseconds).