Action: DIMER

Module colvar
Description Usage
This CV computes the dimer interaction energy for a collection of dimers. used in 0 tutorialsused in 0 eggs
output value type
the dimer interaction energy scalar

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
ATOMS1 atoms The list of atoms representing the first bead of each Dimer being considered by this CV
ATOMS2 atoms The list of atoms representing the second bead of each Dimer being considered by this CV

Further details and examples

This CV computes the dimer interaction energy for a collection of dimers.

Each dimer represents an atom, as described in the dimer paper that is referenced in the bibliography A system of N atoms is thus represented with N dimers, each Dimer being composed of two beads and a virtual site representing its center of mass.

A typical configuration for a dimerized system has the following ordering of atoms:

1    TAG1 X Y Z          N atoms representing the first bead of each Dimer

2    TAG2 X Y Z

...

N    TAGN X Y Z          N atoms representing the second bead of each Dimer

N+1  TAG1 X Y Z

N+2  TAG2 X Y Z

...

2N   TAGN X Y Z          Optional: N atoms representing the center of mass of each Dimer

2N+1 TAG1 X Y Z

2N+2 TAG2 X Y Z

...

3N   TAGN X Y Z          The configuration might go on with un-dimerized atoms (like a solvent)

3N+1

3N+2

...

The Dimer interaction energy is defined between atoms x and N+x, for x=1,...,N and is characterized by two parameters Q and DSIGMA. These are passed as mandatory arguments along with the temperature of the system.

Examples

This line tells Plumed to compute the Dimer interaction energy for every dimer in the system.

Click on the labels of the actions for more information on what each action computes
tested on2.11
dim: DIMERThis CV computes the dimer interaction energy for a collection of dimers. More details TEMPThe temperature (in Kelvin) of the simulation=300 QThe exponent of the dimer potential=0.5 ALLATOMS Use EVERY atom of the system DSIGMAThe interaction strength of the dimer bond=0.002

If the simulation doesn't use virtual sites for the dimers centers of mass, Plumed has to know in order to determine correctly the total number of dimers from the total number of atoms:

Click on the labels of the actions for more information on what each action computes
tested on2.11
dim: DIMERThis CV computes the dimer interaction energy for a collection of dimers. More details TEMPThe temperature (in Kelvin) of the simulation=300 QThe exponent of the dimer potential=0.5 ALLATOMS Use EVERY atom of the system DSIGMAThe interaction strength of the dimer bond=0.002 NOVSITES If present the configuration is without virtual sites at the centroid positions

The NOVSITES flag is not required if one provides the atom serials of each Dimer. These are defined through two lists of atoms provided instead of the ALLATOMS keyword. For example, the Dimer interaction energy of dimers specified by beads (1;23),(5;27),(7;29) is:

Click on the labels of the actions for more information on what each action computes
tested on2.11
dim: DIMERThis CV computes the dimer interaction energy for a collection of dimers. More details TEMPThe temperature (in Kelvin) of the simulation=300 QThe exponent of the dimer potential=0.5 ATOMS1The list of atoms representing the first bead of each Dimer being considered by this CV=1,5,7 ATOMS2The list of atoms representing the second bead of each Dimer being considered by this CV=23,27,29 DSIGMAThe interaction strength of the dimer bond=0.002

Note that the ATOMS1,ATOMS2 keywords can support atom groups and interval notation as defined in GROUP.

In a Replica Exchange simulations the keyword DSIGMA can be used in two ways: if a plumed.n.dat file is provided for each replica, then DSIGMA is passed as a single value, like in the previous examples, and each replica will read its own DSIGMA value. If a unique plumed.dat is given, DSIGMA has to be a list containing a value for each replica. For 4 replicas:

Click on the labels of the actions for more information on what each action computes
tested on2.11
#SETTINGS NREPLICAS=4
dim: DIMERThis CV computes the dimer interaction energy for a collection of dimers. More details TEMPThe temperature (in Kelvin) of the simulation=300 QThe exponent of the dimer potential=0.5 ATOMS1The list of atoms representing the first bead of each Dimer being considered by this CV=1,5,7 ATOMS2The list of atoms representing the second bead of each Dimer being considered by this CV=23,27,29 DSIGMAThe interaction strength of the dimer bond=0.002,0.002,0.004,0.01

Using the CV

The dimer interaction is not coded in the driver program and has to be inserted in the Hamiltonian of the system as a linear RESTRAINT (see RESTRAINT):

Click on the labels of the actions for more information on what each action computes
tested on2.11
dim: DIMERThis CV computes the dimer interaction energy for a collection of dimers. More details TEMPThe temperature (in Kelvin) of the simulation=300 QThe exponent of the dimer potential=0.5 ALLATOMS Use EVERY atom of the system DSIGMAThe interaction strength of the dimer bond=0.002
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=dim ATthe position of the restraint=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=0 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=1 LABELa label for the action so that its output can be referenced in the input to other actions=dimforces

In a replica exchange, Metadynamics (see METAD) can be used on the Dimer CV to reduce the number of replicas. Just keep in mind that METAD SIGMA values should be tuned in the standard way for each replica according to the value of DSIGMA.

References

More information about how this action can be used is available in the following articles: - M. Nava, F. Palazzesi, C. Perego, M. Parrinello, Dimer Metadynamics. Journal of Chemical Theory and Computation. 13, 425–430 (2017)

Syntax

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

Keyword Type Default Description
ATOMS1 input none The list of atoms representing the first bead of each Dimer being considered by this CV
ATOMS2 input none The list of atoms representing the second bead of each Dimer being considered by this CV
DSIGMA compulsory none The interaction strength of the dimer bond
Q compulsory none The exponent of the dimer potential
TEMP compulsory none The temperature (in Kelvin) of the simulation
NUMERICAL_DERIVATIVES optional false calculate the derivatives for these quantities numerically
NOPBC optional false ignore the periodic boundary conditions when calculating distances
ALLATOMS optional false Use EVERY atom of the system
NOVSITES optional false If present the configuration is without virtual sites at the centroid positions