Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. The transformed distance can be compared with a set of reference values in order to calculate the squared distance between two contact maps.

The atoms involved can be specified using

ATOMS

the atoms involved in each of the contacts you wish to calculate. Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one contact will be calculated for each ATOM keyword you specify. You can use multiple instances of this keyword i.e. ATOMS1, ATOMS2, ATOMS3...

Compulsory keywords

SWITCH

The switching functions to use for each of the contacts in your map. You can either specify a global switching function using SWITCH or one switching function for each contact. Details of the various switching functions you can use are provided on switchingfunction. You can use multiple instances of this keyword i.e. SWITCH1, SWITCH2, SWITCH3...

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
SUM	( default=off ) calculate the sum of all the contacts in the input
CMDIST	( default=off ) calculate the distance with respect to the provided reference contant map

REFERENCE

A reference value for a given contact, by default is 0.0 You can either specify a global reference value using REFERENCE or one reference value for each contact. You can use multiple instances of this keyword i.e. REFERENCE1, REFERENCE2, REFERENCE3...

Examples

The following example calculates switching functions based on the distances between atoms 1 and 2, 3 and 4 and 4 and 5. The values of these three switching functions are then output to a file named colvar.

CONTACTMAP ATOMS1=1,2 ATOMS2=3,4 ATOMS3=4,5 ATOMS4=5,6 SWITCH=(RATIONAL R_0=1.5) LABEL=f1
PRINT ARG=f1.* FILE=colvar

The following example calculates the difference of the current contact map with respect to a reference provided.

CONTACTMAP ...
ATOMS1=1,2 REFERENCE1=0.1
ATOMS2=3,4 REFERENCE2=0.5
ATOMS3=4,5 REFERENCE3=0.25
ATOMS4=5,6 REFERENCE4=0.0
SWITCH=(RATIONAL R_0=1.5)
LABEL=cmap
CMDIST
... CONTACTMAP

PRINT ARG=cmap FILE=colvar

(See also PRINT)