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. file is a string for the contact file filename. The contact file has a list formatted as follows: moltype1 at1 moltype2 at2 dist where moltype1 and moltype2 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, and dist 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 the READ section that this condition applies to. This command can be understood as: “Terminate the simulation when molecule molecule fulfills the condition pos val”.

Todo

Add a constant keyword (e.g., like position) before the {pos} argument of term. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/503

time {val}
Specify a time termination condition where val is a floating point number for the trajectory time limit (in picoseconds).