From: Adilah Hussein (hussein_at_fias.uni-frankfurt.de)
Date: Wed Aug 08 2007 - 12:43:00 CDT
I am slightly confused about the temperature control mechanism in NAMD.
Please correct me if I am mistaken:
a) Temperature rescaling
Basically the velocity is rescaled periodically until the target
temperature is reached. So this means if you start with an initial
velocity file, then all the velocities will be rescaled by a constant
every 'x' timesteps until the system reaches the desired temperature.
b) Temperature reassignment
The velocities are assigned to the temperature set in 'reassignTemp' at
the first step, then every 'x' timesteps it will be reassigned that
temperature again. But if 'reassignIncr' is set, then every 'x'
timesteps, the temperature will be reassigned to a
temperature=reassignTemp+some incremental temperature---and this
temperature will continue to increase/decrease throughout the entire
unless you set reassignHold.
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