ADD_BOND

NAME
ADD_BOND - Add the distance between two atoms to the list of reaction coordinates.

SYNOPSIS
ADD_BOND    iat1    iat2    w

DESCRIPTION
This command adds to the list of the reaction coordinates of a metadynamics simulation the distance between atom iat1 and iat2. The numeric order of the atom indices iat1, iat2 is that specified in the topology file (see 10.3). The repulsive potential terms deposed in the space of the reaction coordinates during the simulation (see 6.3.3) will have a width w (in Å) in the direction of this distance.

EXAMPLES
ADD_BOND 1 12 0.2
Add the distance between atom 1 and atom 12 to the list of the reaction coordinates.