Action: DHENERGY

Module	colvar
Description	Usage
Calculate Debye-Huckel interaction energy between the atoms in GROUPA and GROUPB.
output value	type
the value of the DHENERGY	scalar

Details and examples

Calculate Debye-Huckel interaction energy between the atoms in GROUPA and GROUPB.

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

$\frac{1}{4\pi\epsilon_r\epsilon_0} \sum_{i\in A} \sum_{j \in B} q_i q_j \frac{e^{-\kappa |r_{ij}|}}{| r_{ij}|}$

This collective variable can be used to analyze or induce electrostatically driven reactions and is discussed in the paper in the bibliography below. Notice that the value of the DHENERGY is returned in plumed units (see UNITS).

If GROUPB is empty, the variable will be calculated based on the $\frac{N(N-1)}{2}$ pairs in GROUPA. This avoids computing permuted indexes (e.g. pair (i,j) and (j,i)) twice and ensures that the calculation runs 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
dhThe DHENERGY action with label dh calculates the following quantities: Quantity    Type    Description  
dh scalar the value of the DHENERGY: DHENERGYCalculate Debye-Huckel interaction energy between the atoms in GROUPA and GROUPB. More details GROUPAFirst list of atoms=1-10 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=11-20 EPSILON Dielectric constant of solvent=80.0 I Ionic strength (M)=0.1 TEMP Simulation temperature (K)=300.0
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=dh

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
GROUPA	atoms	First list of atoms
GROUPB	atoms	Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)

Full list of keywords

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

Keyword	Type	Default	Description
GROUPA	input	none	First list of atoms
GROUPB	input	none	Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
I	compulsory	1.0	Ionic strength (M)
TEMP	compulsory	300.0	Simulation temperature (K)
EPSILON	compulsory	80.0	Dielectric constant of solvent
NUMERICAL_DERIVATIVESThis keyword do not have examples	optional	false	calculate the derivatives for these quantities numerically
NOPBCThis keyword do not have examples	optional	false	ignore the periodic boundary conditions when calculating distances
SERIALThis keyword do not have examples	optional	false	Perform the calculation in serial - for debug purpose
PAIRThis keyword do not have examples	optional	false	Pair only 1st element of the 1st group with 1st element in the second, etc
NLISTThis keyword do not have examples	optional	false	Use a neighbor list to speed up the calculation
NLISTCELLSThis keyword do not have examples	optional	false	Use a neighbor list to speed up the calculation - use the cell list implementation instead of the classical one
NL_CUTOFFThis keyword do not have examples	optional	not used	The cutoff for the neighbor list
NL_STRIDEThis keyword do not have examples	optional	not used	The frequency with which we are updating the atoms in the neighbor list

References

More information about how this action can be used is available in the following articles:

T. N. Do, P. Carloni, G. Varani, G. Bussi, RNA/Peptide Binding Driven by Electrostatics—Insight from Bidirectional Pulling Simulations. Journal of Chemical Theory and Computation. 9, 1720–1730 (2013)

Quantity	Type	Description
dh	scalar	the value of the DHENERGY