Shortcut: INENVELOPE

Module	volumes
Description	Usage
This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a region where the density of a certain type of atom is high.
output value	type
sum of values of input CVs in regin of interest	scalar

Output components

This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

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

This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a region where the density of a certain type of atom is high.

This collective variable can be used to determine whether atoms are within region where the density of a particular atom type is high. This is achieved by calculating the following function at the point where each atom is located $(x_i,y_i,z_i)$:

$$w_i = 1 - \sigma\left[ \sum_{i=1}^N K\left( \frac{x-x_i}{\sigma_x},\frac{y-y_i}{\sigma_y},\frac{z-z_i}{\sigma_z} \right) \right]$$

Here $\sigma$ is one of the switching functions that is discussed in the documentation for the action LESS_THAN and $K$ is one of the kernel functions that is discussed in the documentation for the action BETWEEN. The sum runs over the atoms specified using the FIELD_ATOMS keyword and a $w_j$ value is calculated for each of the central atoms of the input multicolvar.

The input below shows how this action works in practise. This input calculates a density field from the positions of atoms 1-14400. A vector which has as many elements as atoms that were specified using the ATOMS keyword. The $i$th element of this vector is calculated using the expression above with $(x_i,y_i,z_i)$ being the position of the $i$th atom that was specified using that ATOMS keyword.

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

fiThe INENVELOPE action with label fi calculates the following quantities:
 Quantity   
 Type   
 Description  
fi
vector
vector of numbers between 0 and 1 that measure the degree to which each atom is within the volume of interest: INENVELOPEThis quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a region where the density of a certain type of atom is high. More details ATOMSthe group of atoms that you would like to investigate=14401-74134:3 FIELD_ATOMSthe atom whose positions we are constructing a field from=1-14400 CONTOURa switching funciton that tells PLUMED how large the density should be={RATIONAL D_0=2.0 R_0=1.0} BANDWIDTHthe bandwidths for kernel density esimtation=0.1,0.1,0.1
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=fi FILEthe name of the file on which to output these quantities=colvar

This particular action was developed with the intention of determining whether water molecules had penetrated a membrane or not. The FIELD_ATOMS were thus the atoms of the lipid molecules that made up the membrane and the ATOMS were the oxygens of the water molecules. The vector that is output by this action can be used in all the ways that the vector that is output by the AROUND action is used. In other words, this action can be used to calculate the number of water molecules in the membrane or the average values for a symmetry function for those atoms that are within the membrane.

Syntax

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