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

Input

The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Further 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

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)

Syntax

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