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 [74]. 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.

- 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. |

- Examples

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

dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=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:

dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002 NOVSITES

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:

dim: DIMER TEMP=300 Q=0.5 ATOMS1=1,5,7 ATOMS2=23,27,29 DSIGMA=0.002

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:

#SETTINGS NREPLICAS=4 dim: DIMER TEMP=300 Q=0.5 ATOMS1=1,5,7 ATOMS2=23,27,29 DSIGMA=0.002,0.002,0.004,0.01

- 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):

dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002 RESTRAINT ARG=dim AT=0 KAPPA=0 SLOPE=1 LABEL=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.