2.4. PLOTS#
2.4.1. MD Graphics#
The PLOTS module performs graphical analysis of simulated properties, through a unified interface for the ORCA and GROMACS programs. It can be used from the command:
plots ⟨simbox.ext⟩ [⟨-options⟩]
where ext is one of the extensions recognized by Solvate Suite (out [ORCA], or log [GROMACS]), and “-options” a set of the configurations for the simulation execution.
Note
Simply type plots in the terminal and press enter to see the full list of execution options for the module.
2.4.2. Execution Options#
plots ⟨inputs.ext⟩ [⟨-options⟩]
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Formatted plots:
+ ----------------------------------------------------------
-tim : Plot graphs for params vs simulation time. [-tm]
-stp : Plot graphs for params vs simulation step. [-st]
-cnv = Cumulative value to be highlighted in RDF analysis. [-cv]
+ ----------------------------------------------------------
General plots:
+ ----------------------------------------------------------
-csv : Load an unformated general plot. [-cs]
-plt : Plot y versus x as lines (default). [-pt]
-sct : A scatter plot of y vs x with varying marker size/color. [-sc]
-bar : Make a bar plot. [-br]
-stm : Create a stem plot. [-st]
+ ----------------------------------------------------------
-sma : Simple moving average to the extracted RDF data. [-sm]
+ ----------------------------------------------------------
Saving plots:
+ ----------------------------------------------------------
-bak : Save generated graphs (without iterative interface). [-bk]
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⁽*⁾ ext = dat, rms, rdf, csv, nmr
2.4.3. Quickstart Examples#
Under construction…