Shortcut: CONVERT_TO_FES

Module	gridtools
Description	Usage
Convert a histogram to a free energy surface.
output value	type
the free energy surface	grid

Details and examples

Convert a histogram to a free energy surface.

This action allows you to take a free energy surface that was calculated using the HISTOGRAM action and to convert it to a free energy surface. This transformation performed by doing:

$F(x) = -k_B T \ln H(x)$

The free energy calculated on a grid is output by this action and can be printed using DUMPGRID

Examples

This is a typical example showing how CONVERT_TO_FES might be used when post processing a trajectory. The input below calculates the free energy as a function of the distance between atom 1 and atom 2. This is done by accumulating a histogram as a function of this distance using kernel density estimation and the HISTOGRAM action. All the data within this trajectory is used in the construction of this HISTOGRAM. Finally, once all the data has been read in, the histogram is converted to a free energy using the formula above and the free energy is output to a file called fes.dat

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

xThe DISTANCE action with label x calculates the following quantities: Quantity    Type    Description  
x scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2
hA1The HISTOGRAM action with label hA1 calculates the following quantities: Quantity    Type    Description  
hA1 grid the estimate of the histogram as a function of the argument that was obtained: HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details ARGthe quantities that are being used to construct the histogram=x GRID_MIN the lower bounds for the grid=0.0 GRID_MAX the upper bounds for the grid=3.0 GRID_BINthe number of bins for the grid=100 BANDWIDTHthe bandwidths for kernel density esimtation=0.1
hA1: HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details ARGthe quantities that are being used to construct the histogram=x GRID_MIN the lower bounds for the grid=0.0 GRID_MAX the upper bounds for the grid=3.0 GRID_BINthe number of bins for the grid=100 BANDWIDTHthe bandwidths for kernel density esimtation=0.1  NORMALIZATION This controls how the data is normalized it can be set equal to true, false or ndata=ndata STRIDE the frequency with which to store data for averaging=1 CLEAR the frequency with whihc to clear the data that is being averaged=0
# PLUMED interprets the command:
# hA1: HISTOGRAM ARG=x GRID_MIN=0.0 GRID_MAX=3.0 GRID_BIN=100 BANDWIDTH=0.1
# as follows (Click the red comment above to revert to the short version of the input):
hA1_weightThe CONSTANT action with label hA1_weight calculates the following quantities: Quantity    Type    Description  
hA1_weight scalar the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=1
hA1_kdeThe KDE action with label hA1_kde calculates the following quantities: Quantity    Type    Description  
hA1_kde grid a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: KDECreate a histogram from the input scalar/vector/matrix using KDE More details ARGthe label for the value that should be used to construct the histogram=x  GRID_MIN the lower bounds for the grid=0.0 GRID_MAX the upper bounds for the grid=3.0 GRID_BINthe number of bins for the grid=100 BANDWIDTHthe bandwidths for kernel density esimtation=0.1
hA1_kdepThe CUSTOM action with label hA1_kdep calculates the following quantities: Quantity    Type    Description  
hA1_kdep grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hA1_kde,hA1_weight FUNCthe function you wish to evaluate=x*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hA1_uThe ACCUMULATE action with label hA1_u calculates the following quantities: Quantity    Type    Description  
hA1_u grid a sum calculated from the time series of the input quantity: ACCUMULATESum the elements of this value over the course of the trajectory More details ARGthe label of the argument that is being added to on each timestep=hA1_kdep STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 CLEAR the frequency with which to clear all the accumulated data=0 
hA1_nsumThe ACCUMULATE action with label hA1_nsum calculates the following quantities: Quantity    Type    Description  
hA1_nsum scalar a sum calculated from the time series of the input quantity: ACCUMULATESum the elements of this value over the course of the trajectory More details ARGthe label of the argument that is being added to on each timestep=hA1_weight STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 CLEAR the frequency with which to clear all the accumulated data=0 
hA1The CUSTOM action with label hA1 calculates the following quantities: Quantity    Type    Description  
hA1 grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hA1_u,hA1_nsum FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- ffThe CONVERT_TO_FES action with label ff calculates the following quantities: Quantity    Type    Description  
ff grid the free energy surface: CONVERT_TO_FESConvert a histogram to a free energy surface. This action is a shortcut. More details ARGthe histogram that you would like to convert into a free energy surface=hA1 TEMPthe temperature at which you are operating=300
# PLUMED interprets the command:
# ff: CONVERT_TO_FES ARG=hA1 TEMP=300
# as follows (Click the red comment above to revert to the short version of the input):
ffThe CUSTOM action with label ff calculates the following quantities: Quantity    Type    Description  
ff grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hA1 FUNCthe function you wish to evaluate=-2.49434*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details ARGthe label for the grid that you would like to output=ff FILE the file on which to write the grid=fes.dat

In this example we ensure that all the reported values of the free energy are non-negative by finding the minimum in the free energy and setting reporting the free energies relative to the estimate of the value of the free energy at this minimum.

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

xThe DISTANCE action with label x calculates the following quantities: Quantity    Type    Description  
x scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2
hA1The HISTOGRAM action with label hA1 calculates the following quantities: Quantity    Type    Description  
hA1 grid the estimate of the histogram as a function of the argument that was obtained: HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details ARGthe quantities that are being used to construct the histogram=x GRID_MIN the lower bounds for the grid=0.0 GRID_MAX the upper bounds for the grid=3.0 GRID_BINthe number of bins for the grid=100 BANDWIDTHthe bandwidths for kernel density esimtation=0.1
hA1: HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details ARGthe quantities that are being used to construct the histogram=x GRID_MIN the lower bounds for the grid=0.0 GRID_MAX the upper bounds for the grid=3.0 GRID_BINthe number of bins for the grid=100 BANDWIDTHthe bandwidths for kernel density esimtation=0.1  NORMALIZATION This controls how the data is normalized it can be set equal to true, false or ndata=ndata STRIDE the frequency with which to store data for averaging=1 CLEAR the frequency with whihc to clear the data that is being averaged=0
# PLUMED interprets the command:
# hA1: HISTOGRAM ARG=x GRID_MIN=0.0 GRID_MAX=3.0 GRID_BIN=100 BANDWIDTH=0.1
# as follows (Click the red comment above to revert to the short version of the input):
hA1_weightThe CONSTANT action with label hA1_weight calculates the following quantities: Quantity    Type    Description  
hA1_weight scalar the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=1
hA1_kdeThe KDE action with label hA1_kde calculates the following quantities: Quantity    Type    Description  
hA1_kde grid a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: KDECreate a histogram from the input scalar/vector/matrix using KDE More details ARGthe label for the value that should be used to construct the histogram=x  GRID_MIN the lower bounds for the grid=0.0 GRID_MAX the upper bounds for the grid=3.0 GRID_BINthe number of bins for the grid=100 BANDWIDTHthe bandwidths for kernel density esimtation=0.1
hA1_kdepThe CUSTOM action with label hA1_kdep calculates the following quantities: Quantity    Type    Description  
hA1_kdep grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hA1_kde,hA1_weight FUNCthe function you wish to evaluate=x*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hA1_uThe ACCUMULATE action with label hA1_u calculates the following quantities: Quantity    Type    Description  
hA1_u grid a sum calculated from the time series of the input quantity: ACCUMULATESum the elements of this value over the course of the trajectory More details ARGthe label of the argument that is being added to on each timestep=hA1_kdep STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 CLEAR the frequency with which to clear all the accumulated data=0 
hA1_nsumThe ACCUMULATE action with label hA1_nsum calculates the following quantities: Quantity    Type    Description  
hA1_nsum scalar a sum calculated from the time series of the input quantity: ACCUMULATESum the elements of this value over the course of the trajectory More details ARGthe label of the argument that is being added to on each timestep=hA1_weight STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 CLEAR the frequency with which to clear all the accumulated data=0 
hA1The CUSTOM action with label hA1 calculates the following quantities: Quantity    Type    Description  
hA1 grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hA1_u,hA1_nsum FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- ffThe CONVERT_TO_FES action with label ff calculates the following quantities: Quantity    Type    Description  
ff grid the free energy surface: CONVERT_TO_FESConvert a histogram to a free energy surface. This action is a shortcut. More details ARGthe histogram that you would like to convert into a free energy surface=hA1 TEMPthe temperature at which you are operating=300 MINTOZERO set the minimum in the free energy to be equal to zero
# PLUMED interprets the command:
# ff: CONVERT_TO_FES ARG=hA1 TEMP=300 MINTOZERO
# as follows (Click the red comment above to revert to the short version of the input):
ff_unzThe CUSTOM action with label ff_unz calculates the following quantities: Quantity    Type    Description  
ff_unz grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hA1 FUNCthe function you wish to evaluate=-2.49434*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ff_minThe FIND_GRID_MINIMUM action with label ff_min calculates the following quantities: Quantity    Type    Description  
ff_min.x_opt scalar the values of the arguments of the function at the optimum can be referenced elsewhere in the input file by using the names of the arguments followed by the string _opt This particular component measures this quantity for the input CV named x
ff_min.optval scalar the value of the function at the optimum: FIND_GRID_MINIMUMFind the point with the lowest value of the function on the grid More details ARGthe label for the function on the grid that you would like to find the optimum in=ff_unz
ffThe CUSTOM action with label ff calculates the following quantities: Quantity    Type    Description  
ff grid the grid obtained by doing an element-wise application of an arbitrary function to the input grid: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ff_unz,ff_min.optval FUNCthe function you wish to evaluate=x-y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details ARGthe label for the grid that you would like to output=ff FILE the file on which to write the grid=fes.dat

Full list of keywords

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

Keyword	Type	Default	Description
ARG	compulsory	none	the histogram that you would like to convert into a free energy surface
TEMP	optional	not used	the temperature at which you are operating
MINTOZERO	optional	false	set the minimum in the free energy to be equal to zero

deprecated keywords

The keywords in the following table can still be used with this action but have been deprecated

Keyword	Description
GRID	You should use ARG instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only

Quantity	Type	Description
x	scalar	the DISTANCE between this pair of atoms