Action: CONTACTMAP

Module colvar
Description Usage
Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. used in 1 tutorialsused in 20 eggs
output value type
the sum of all the switching function on all the distances scalar

Output components

This action calculates the values in the following table. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Name Type Description
contact scalar By not using SUM or CMDIST each contact will be stored in a component

Input

The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword Type Description
ATOMS atoms the atoms involved in each of the contacts you wish to calculate

Further details and examples

Calculate the distances between a number of pairs of atoms and transform each distance by a switching function.

This CV calculates a series of distances between pairs of atoms and transforms them by a switching function. The transformed distance can be compared with a reference value in order to calculate the squared distance between two contact maps. Each distance can also be weighted for a given value. CONTACTMAP can be used together with FUNCPATHMSD to define a path in contactmap space as was done in the 2008 paper by Bonomi that is cited below.

The individual contact map distances related to each contact can be accessed as components named cm.contact-1, cm.contact-2, etc, assuming that the label of the CONTACTMAP is cm.

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.

Click on the labels of the actions for more information on what each action computes
tested on2.11
f1: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ATOMS1the atoms involved in each of the contacts you wish to calculate=1,2 ATOMS2the atoms involved in each of the contacts you wish to calculate=3,4 ATOMS3the atoms involved in each of the contacts you wish to calculate=4,5 ATOMS4the atoms involved in each of the contacts you wish to calculate=5,6 SWITCHThe switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.5}
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=f1.* FILEthe name of the file on which to output these quantities=colvar

The following example calculates the difference of the current contact map with respect to a reference provided. In this case REFERENCE is the fraction of contact that is formed (i.e. the distance between two atoms transformed with the SWITCH), while R_0 is the contact distance. WEIGHT gives the relative weight of each contact to the final distance measure.

Click on the labels of the actions for more information on what each action computes
tested on2.11
cmap: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
  ATOMS1the atoms involved in each of the contacts you wish to calculate=1,2 REFERENCE1A reference value for a given contact, by default is 0=0.1 WEIGHT1A weight value for a given contact, by default is 1=0.5
  ATOMS2the atoms involved in each of the contacts you wish to calculate=3,4 REFERENCE2A reference value for a given contact, by default is 0=0.5 WEIGHT2A weight value for a given contact, by default is 1=1.0
  ATOMS3the atoms involved in each of the contacts you wish to calculate=4,5 REFERENCE3A reference value for a given contact, by default is 0=0.25 WEIGHT3A weight value for a given contact, by default is 1=1.0
  ATOMS4the atoms involved in each of the contacts you wish to calculate=5,6 REFERENCE4A reference value for a given contact, by default is 0=0.0 WEIGHT4A weight value for a given contact, by default is 1=0.5
  SWITCHThe switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.5}
  CMDIST calculate the distance with respect to the provided reference contact map
...

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cmap FILEthe name of the file on which to output these quantities=colvar

The next example calculates calculates fraction of native contacts (Q) for Trp-cage mini-protein. R_0 is the distance at which the switch function is guaranteed to be 1.0 – it doesn't really matter for Q and should be something very small, like 1 A. REF is the reference distance for the contact, e.g. the distance from a crystal structure. LAMBDA is the tolerance for the distance – if set to 1.0, the contact would have to have exactly the reference value to be formed; instead for lambda values of 1.5–1.8 are usually used to allow some slack. BETA is the softness of the switch function, default is 50nm. WEIGHT is the 1/(number of contacts) giving equal weight to each contact.

When using native contact Q switch function, please cite the 2013 paper from Best from the bibliography below

Click on the labels of the actions for more information on what each action computes
tested on2.11
# The full (much-longer) example available in regtest/basic/rt72/

cmap: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
   ATOMS1the atoms involved in each of the contacts you wish to calculate=1,67 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.4059} WEIGHT1A weight value for a given contact, by default is 1=0.003597
   ATOMS2the atoms involved in each of the contacts you wish to calculate=1,68 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.4039} WEIGHT2A weight value for a given contact, by default is 1=0.003597
   ATOMS3the atoms involved in each of the contacts you wish to calculate=1,69 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.3215} WEIGHT3A weight value for a given contact, by default is 1=0.003597
   ATOMS4the atoms involved in each of the contacts you wish to calculate=5,61 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.4277} WEIGHT4A weight value for a given contact, by default is 1=0.003597
   ATOMS5the atoms involved in each of the contacts you wish to calculate=5,67 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.3851} WEIGHT5A weight value for a given contact, by default is 1=0.003597
   ATOMS6the atoms involved in each of the contacts you wish to calculate=5,68 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.3811} WEIGHT6A weight value for a given contact, by default is 1=0.003597
   ATOMS7the atoms involved in each of the contacts you wish to calculate=5,69 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.3133} WEIGHT7A weight value for a given contact, by default is 1=0.003597
   SUM calculate the sum of all the contacts in the input
...

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cmap FILEthe name of the file on which to output these quantities=colvar

References

More information about how this action can be used is available in the following articles: - M. Bonomi, D. Branduardi, F. L. Gervasio, M. Parrinello, The Unfolded Ensemble and Folding Mechanism of the C-Terminal GB1 β-Hairpin. Journal of the American Chemical Society. 130, 13938–13944 (2008) - R. B. Best, G. Hummer, W. A. Eaton, Native contacts determine protein folding mechanisms in atomistic simulations. Proceedings of the National Academy of Sciences. 110, 17874–17879 (2013)

Syntax

The following table describes the keywords and options that can be used with this action

Keyword Type Default Description
ATOMS input none the atoms involved in each of the contacts you wish to calculate
SWITCH compulsory none The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.
NUMERICAL_DERIVATIVES optional false calculate the derivatives for these quantities numerically
NOPBC optional false ignore the periodic boundary conditions when calculating distances
REFERENCE optional not used A reference value for a given contact, by default is 0
WEIGHT optional not used A weight value for a given contact, by default is 1
SUM optional false calculate the sum of all the contacts in the input
CMDIST optional false calculate the distance with respect to the provided reference contact map
SERIAL optional false Perform the calculation in serial - for debug purpose