term¶
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.
fileis a string for the contact file filename. The contact file has a list formatted as follows:moltype1 at1 moltype2 at2 distwheremoltype1andmoltype2are indices of the molecular types,at1is the index of an atom from the first molecular type,at2is the index of an atom from the second molecular type, anddistis the maximum distance between the two atoms that defines the contact.padis 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
posis one of the following options:x<=, x>=, y<=, y>=, z<=, z>=, r<=, r>=.valis the value along the given axis to check against.moleculeis the molecule index (1 based) according to the order of molecules listed in theREADsection that this condition applies to. This command can be understood as: “Terminate the simulation when moleculemoleculefulfills the conditionposval”.Todo
Add a constant keyword (e.g., like
position) before the{pos}argument ofterm. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/503time {val}- Specify a time termination condition where
valis a floating point number for the trajectory time limit (in picoseconds).