Download Desmond Users Guide - Gemini Computing Cluster

Desmond Users Guide, Release 3.4.0 / 0.7.1
app.plugin = {
list = [ ... slow fast ... ]
slow = {
type = pprofile
first = 0
interval = 10
eval_interval = 0.2
nslabs = 8
name = pp-slow.dtr
include = [far_terms]
}
fast = { # fast
type = pprofile
first = 0
interval = 10
eval_interval = 0.01
nslabs = 8
name = pp-fast.dtr
exclude = [far_terms]
}
}
4.6.10 randomize_velocities
The randomize_velocities plugin periodically thermalizes velocities. Configuration is shown in:
app.plugin = {
list = [ ... key ... ]
key = {
type = randomize_velocities
first = tf
interval = ti
seed = s
temperature = T
}
}
You can use this plugin to perform initial velocity randomization, by setting the value of first to zero, interval
to infinity, and temperature to the desired temperature. The plugin can also serve as a rough implementation of an
Andersen thermostat.
Table 4.18: Configuration for randomize_velocities
name
first
interval
seed
temperature
description
First time for this action. [Time]
Time between actions. [Time]
Seed for the random number generator. [Integer]
The target temperature. [temperature]
4.6.11 remove_com_motion
The remove_com_motion plugin periodically removes net center of mess motion from the system velocities.
Configuration is shown in:
4.6. Configuring the built-in plugins
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