Action: EXTERNAL
Module | bias |
---|---|
Description | Usage |
Calculate a restraint that is defined on a grid that is read during start up |
Input
The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.
Keyword | Type | Description |
---|---|---|
ARG | scalar | the labels of the scalars on which the bias will act |
Further details and examples
Calculate a restraint that is defined on a grid that is read during start up
In this action you define an external potential that you would like to use as a bias in a file. This file contains the value of your bias potential on a grid of points. The instantaneous value of the bias potential is then computed via interpolation.
The following input illustrates how this works in practice. Here the external potential is
defined in the file extras/1d_bias.dat
. This potential acts on the distance between atoms 3 and 5.
#SETTINGS INPUTFILES=extras/1d_bias.grid d1 : DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,5 mEXTERNALCalculate a restraint that is defined on a grid that is read during start up This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=d1 FILEthe name of the file containing the external potential=extras/1d_bias.gridClick here to see an extract from this file.:
As you can see from the example above, the file that is input to the EXTERNAL command contains the value of the function and its derivative on a grid of points. This file has the grid format that is discussed in the documentation for DUMPGRID.
You can also include grids that are a function of more than one collective variable. For instance the following would be the input for an external potential acting on two torsional angles:
#SETTINGS INPUTFILES=extras/2d_bias.grid t1 : TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=4,5,6,7 t2 : TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=6,7,8,9 extEXTERNALCalculate a restraint that is defined on a grid that is read during start up This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=t1,t2 FILEthe name of the file containing the external potential=extras/2d_bias.gridClick here to see an extract from this file.:
Please note the order that the order of arguments in the plumed.dat file must be the same as the order of arguments in the header of the grid file.
Syntax
The following table describes the keywords and options that can be used with this action
Keyword | Type | Default | Description |
---|---|---|---|
ARG | input | none | the labels of the scalars on which the bias will act |
FILE | compulsory | none | the name of the file containing the external potential |
SCALE | compulsory | 1.0 | a factor that multiplies the external potential, useful to invert free energies |
NUMERICAL_DERIVATIVES | optional | false | calculate the derivatives for these quantities numerically |
NOSPLINE | optional | false | specifies that no spline interpolation is to be used when calculating the energy and forces due to the external potential |
SPARSE | optional | false | specifies that the external potential uses a sparse grid |