DIMER

This is part of the colvar module

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

Each dimer represents an atom, as described in the dimer paper [80]. A system of N atoms is thus represented with N dimers, each Dimer being composed of two beads and eventually 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

dim: DIMER 
TEMP
compulsory keyword 
The temperature (in Kelvin) of the simulation. 
=300 
Q
compulsory keyword 
The exponent of the dimer potential. 
=0.5 
ALLATOMS
( default=off ) Use EVERY atom of the system. 
 
DSIGMA
compulsory keyword 
The interaction strength of the dimer bond. 
=0.002 The DIMER action with label dim calculates a single scalar value

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

dim: DIMER 
TEMP
compulsory keyword 
The temperature (in Kelvin) of the simulation. 
=300 
Q
compulsory keyword 
The exponent of the dimer potential. 
=0.5 
ALLATOMS
( default=off ) Use EVERY atom of the system. 
 
DSIGMA
compulsory keyword 
The interaction strength of the dimer bond. 
=0.002 
NOVSITES
( default=off ) If present the configuration is without virtual sites at the centroid
positions. 
 The DIMER action with label dim calculates a single scalar value

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

dim: DIMER 
TEMP
compulsory keyword 
The temperature (in Kelvin) of the simulation. 
=300 
Q
compulsory keyword 
The exponent of the dimer potential. 
=0.5 
ATOMS1
 could not find this keyword 
=1,5,7 
ATOMS2
 could not find this keyword 
=23,27,29 
DSIGMA
compulsory keyword 
The interaction strength of the dimer bond. 
=0.002 The DIMER action with label dim calculates a single scalar value

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

In a Replica Exchange simulation 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

#SETTINGS NREPLICAS=4
dim: DIMER 
TEMP
compulsory keyword 
The temperature (in Kelvin) of the simulation. 
=300 
Q
compulsory keyword 
The exponent of the dimer potential. 
=0.5 
ATOMS1
 could not find this keyword 
=1,5,7 
ATOMS2
 could not find this keyword 
=23,27,29 
DSIGMA
compulsory keyword 
The interaction strength of the dimer bond. 
=0.002,0.002,0.004,0.01 The DIMER action with label dim calculates a single scalar value

Usage of 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

contract shortcuts

dim: DIMER 
TEMP
compulsory keyword 
The temperature (in Kelvin) of the simulation. 
=300 
Q
compulsory keyword 
The exponent of the dimer potential. 
=0.5 
ALLATOMS
( default=off ) Use EVERY atom of the system. 
 
DSIGMA
compulsory keyword 
The interaction strength of the dimer bond. 
=0.002 The DIMER action with label dim calculates a single scalar value
dimforces: RESTRAINT 
ARG
the values the harmonic restraint acts upon. 
=dim 
AT
compulsory keyword 
the position of the restraint 
=0 
KAPPA
compulsory keyword ( default=0.0 )
specifies that the restraint is harmonic and what the values of the force constants
on each of the variables are 
=0 
SLOPE
compulsory keyword ( default=0.0 )
specifies that the restraint is linear and what the values of the force constants
on each of the variables are 
=1 The RESTRAINT action with label dimforces calculates the following quantities:

 Quantity   
 Description  
dimforces.bias
the instantaneous value of the bias potential
dimforces.force2
the instantaneous value of the squared force due to this bias potential

dim: DIMER 
TEMP
compulsory keyword 
The temperature (in Kelvin) of the simulation. 
=300 
Q
compulsory keyword 
The exponent of the dimer potential. 
=0.5 
ALLATOMS
( default=off ) Use EVERY atom of the system. 
 
DSIGMA
compulsory keyword 
The interaction strength of the dimer bond. 
=0.002 The DIMER action with label dim calculates a single scalar value

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.

Glossary of keywords and components

Description of components

By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity	Description
.#!value	the dimer interaction energy

The atoms involved can be specified using

ATOMS1	The list of atoms representing the first bead of each Dimer being considered by this CV. Used if ALLATOMS flag is missing. For more information on how to specify lists of atoms see Groups and Virtual Atoms
ATOMS2	The list of atoms representing the second bead of each Dimer being considered by this CV. Used if ALLATOMS flag is missing. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Compulsory keywords

DSIGMA	The interaction strength of the dimer bond.
Q	The exponent of the dimer potential.
TEMP	The temperature (in Kelvin) of the simulation.

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
ALLATOMS	( default=off ) Use EVERY atom of the system. Overrides ATOMS keyword.
NOVSITES	( default=off ) If present the configuration is without virtual sites at the centroid positions.