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Output the function on the grid to a file with the PLUMED grid format.
PLUMED provides a number of actions that calculate the values of functions on grids. For instance, whenver you calculate a free energy as a function of a collective variable using HISTOGRAM and CONVERT_TO_FES you will generally want to output the value of the free energy at a number of points on a discrete grid that covers the CV space uniformly. Alternatively you may want to calculate what value some symmetry function takes at different points inside your simulation cell using MULTICOLVARDENS.
This action allows you to output these functions calculated on a grid using a format that can be read in using gnuplot and other such plotting programs. The file output using this action will have a header that contains some essential information about the function plotted and that looks something like this:
#! FIELDS x y hA1 dhA1_x dhA1_x #! SET normalisation 2.0000 #! SET min_x 0.0 #! SET max_x 3.0 #! SET nbins_x 100 #! SET periodic_x false #! SET min_y 0.0 #! SET max_y 3.0 #! SET nbins_y 100 #! SET periodic_y false
The header shown here tells us that we have grid showing the values that a function with two arguments x and y takes at various points in our cell. The lines beheath the first line then tell us a little bit about these two input arguments.
The remaining lines of the file give us information on the positions of our grid points and the value the function and its partial derivatives with respect to x and y. If the header is as above a list of values of the function that have x=0 and 100 values of y between 0.0 and 3.0 will be provided. This block of data will be followed with a blank line. There will then be a second block of values which will all have been evaluated the same value of x and all possible values for y. This block is then followed by a blank line again and this pattern continues until all points of the grid have been covered.
| GRID | the action that creates the grid you would like to output |
| STRIDE | ( default=0 ) the frequency with which the grid should be output to the file. The default value of 0 ensures that the grid is only output at the end of the trajectory |
| FILE | ( default=density ) the file on which to write the grid. |
| FMT | the format that should be used to output real numbers |
The following input monitors two torsional angles during a simulation and outputs a continuos histogram as a function of them at the end of the simulation.
TORSION ATOMS=1,2,3,4 LABEL=r1 TORSION ATOMS=2,3,4,5 LABEL=r2 HISTOGRAM ... ARG=r1,r2 GRID_MIN=-3.14,-3.14 GRID_MAX=3.14,3.14 GRID_BIN=200,200 BANDWIDTH=0.05,0.05 LABEL=hh ... HISTOGRAM DUMPGRID GRID=hh FILE=histo
The following input monitors two torsional angles during a simulation and outputs a discrete histogram as a function of them at the end of the simulation.
TORSION ATOMS=1,2,3,4 LABEL=r1 TORSION ATOMS=2,3,4,5 LABEL=r2 HISTOGRAM ... ARG=r1,r2 KERNEL=DISCRETE GRID_MIN=-3.14,-3.14 GRID_MAX=3.14,3.14 GRID_BIN=200,200 LABEL=hh ... HISTOGRAM DUMPGRID GRID=hh FILE=histo
The following input monitors two torsional angles during a simulation and outputs the histogram accumulated thus far every 100000 steps.
TORSION ATOMS=1,2,3,4 LABEL=r1 TORSION ATOMS=2,3,4,5 LABEL=r2 HISTOGRAM ... ARG=r1,r2 GRID_MIN=-3.14,-3.14 GRID_MAX=3.14,3.14 GRID_BIN=200,200 BANDWIDTH=0.05,0.05 LABEL=hh ... HISTOGRAM DUMPGRID GRID=hh FILE=histo STRIDE=100000
The following input monitors two torsional angles during a simulation and outputs a separate histogram for each 100000 steps worth of trajectory. Notice how the CLEAR keyword is used here and how it is not used in the previous example.
TORSION ATOMS=1,2,3,4 LABEL=r1 TORSION ATOMS=2,3,4,5 LABEL=r2 HISTOGRAM ... ARG=r1,r2 CLEAR=100000 GRID_MIN=-3.14,-3.14 GRID_MAX=3.14,3.14 GRID_BIN=200,200 BANDWIDTH=0.05,0.05 GRID_WFILE=histo LABEL=hh ... HISTOGRAM DUMPGRID GRID=hh FILE=histo STRIDE=100000
1.8.14