DHENERGY

This is part of the colvar module

Calculate Debye-Huckel interaction energy among GROUPA and GROUPB.

This variable calculates the electrostatic interaction among GROUPA and GROUPB using a Debye-Huckel approximation defined as

\[ \frac{1}{4\pi\epsilon_r\epsilon_0} \sum_{i\in A} \sum_{j \in B} q_i q_j \frac{e^{-\kappa |{\bf r}_{ij}|}}{|{\bf r}_{ij}|} \]

This collective variable can be used to analyze or induce electrostatically driven reactions [39]. Notice that the value of the DHENERGY is returned in plumed units (see UNITS).

If GROUPB is empty, it will sum the N*(N-1)/2 pairs in GROUPA. This avoids computing twice permuted indexes (e.g. pair (i,j) and (j,i)) thus running at twice the speed.

Notice that if there are common atoms between GROUPA and GROUPB their interaction is discarded.

Examples

Click on the labels of the actions for more information on what each action computes

# this is printing the electrostatic interaction between two groups of atoms
dh: DHENERGY 
GROUPA
First list of atoms. 
=1-10 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted). 
=11-20 
EPSILON
compulsory keyword ( default=80.0 )
Dielectric constant of solvent 
=80.0 
I
compulsory keyword ( default=1.0 )
Ionic strength (M) 
=0.1 
TEMP
compulsory keyword ( default=300.0 )
Simulation temperature (K) 
=300.0 The DHENERGY action with label dh calculates a single scalar value
PRINT 
ARG
compulsory keyword 
the labels of the values that you would like to print to the file 
=dh The PRINT action with label 

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 value of the DHENERGY

The atoms involved can be specified using

GROUPA	First list of atoms. For more information on how to specify lists of atoms see Groups and Virtual Atoms
GROUPB	Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted). For more information on how to specify lists of atoms see Groups and Virtual Atoms

Compulsory keywords

I	( default=1.0 ) Ionic strength (M)
TEMP	( default=300.0 ) Simulation temperature (K)
EPSILON	( default=80.0 ) Dielectric constant of solvent

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
SERIAL	( default=off ) Perform the calculation in serial - for debug purpose
PAIR	( default=off ) Pair only 1st element of the 1st group with 1st element in the second, etc
NLIST	( default=off ) Use a neighbor list to speed up the calculation
NL_CUTOFF	The cutoff for the neighbor list
NL_STRIDE	The frequency with which we are updating the atoms in the neighbor list