mdadash.backend.analyses.vdos

Vibrational Density of States (VDoS)

Classes

VDoS()

Vibrational Density of States

class mdadash.backend.analyses.vdos.VDoS

Bases: WidgetBase

Vibrational Density of States

This widget calculates Vibrational Density of States (VDoS) from Velocity Autocorrelation Function (VACF).

SlidingWindowACF is used to calculate a mass weighted VACF from which VDoS is calculated.

Important

VDoS requires trajectories to include velocities.

Inputs

Run mode

The mode in which the widget is run - serial or parallel

Default: serial

Selection

The MDAnalysis selection phrase to run this analysis on

Default: protein

Custom title

Custom title for the output plot

Default: ‘’

Plot refresh frequency

The frequency with which the plot is refreshed (every n frames). This only applies when the run frequency is every-frame

Default: 1

Output

Here is an example output plot of this widget:

Tip

This widget can run in parallel

apply_parallel_results(values)

apply_parallel_results() handler

description = 'Vibrational Density of States'

get_parallel_job()

get_parallel_job() handler

name = 'VDoS'

on_input_change(attribute, _old_value, new_value)

on_input_change() handler

on_post_connect()

on_post_connect() handler

on_post_create()

on_post_create() handler

run_batch()

batch run handler

run_every_frame()

run_every_frame() handler