Package schrodinger :: Package application :: Package desmond :: Module meta :: Class CVzdist

Class CVzdist

CV --+
     |
    CVzdist

This collective variable reports an absolute Z-distance. this CV is used for membrane penetration studies.

Instance Methods

[hide private]

__init__(self, atomlist, width, wall, floor)

getMExpr(self, model, cvname)

Class Variables

[hide private]

cvzdist_template = '\n# Z-dist definition\n%(cvname)s_g0 = cen...

cvdist_wall_template = '\n# the upper bound, wall params for %...

cvdist_floor_template = '\n# lower bound wall or \'floor\' par...

Method Details

[hide private]

init(self, atomlist, width, wall, floor)
(Constructor)

Overrides: CV.__init__

getMExpr(self, model, cvname)

Overrides: CV.getMExpr

Class Variable Details

[hide private]

cvzdist_template

Value:

'''
# Z-dist definition
%(cvname)s_g0 = center_of_mass ( %(atomlist)s );
%(cvname)s  = %(cvname)s_g0[2];
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) );
'''

Class CVzdist

__init__(self, atomlist, width, wall, floor) (Constructor)

getMExpr(self, model, cvname)

cvzdist_template

cvdist_wall_template

cvdist_floor_template

init(self, atomlist, width, wall, floor)
(Constructor)