Class CVDist

Overrides: CV.__init__

Overrides: CV.getMExpr

cvdist_template

Value:

""" # distance definition %(cvname)s_p0 = %(p0_atomsel)s; %(cvname)s_p1 = %(p1_atomsel)s; %(cvname)s = dist(%(cvname)s_p0, %(cvname)s_p1); print ("%(cvname)s", %(cvname)s); # the width for %(cvname)s will be set to: %(width)s """

cvdist_grp_template

Value:

""" # distance definition for group of atoms %(cvname)s_g0 = center_of_mass ( %(p0_atomsel)s ); %(cvname)s_g1 = center_of_mass ( %(p1_atomsel)s ); %(cvname)s = norm(min_image(%(cvname)s_g0 - %(cvname)s_g1)); print ("%(cvname)s", %(cvname)s); # the width for %(cvname)s will be set to: %(width)s """

cvdist_wall_template

Value:

""" # the upper bound, wall params for %(cvname)s are: width is 0.2; # location at %(wall)f; hight is 1000 %(cvname)s_wall = 1000 / (1 + exp(( %(wall)f - %(cvname)s) / 0.2) ); """

cvdist_floor_template

Value:

""" # lower bound wall or 'floor' params for %(cvname)s are: width is 0.2; # location at %(floor)f; # hight is 1000 %(cvname)s_floor = 1000 / (1 + exp((%(cvname)s - %(floor)f) / 0.2) ); """