From: Alessio Alexiadis (sersunzo_at_yahoo.com)
Date: Thu May 24 2007 - 02:59:31 CDT
I’m trying to figure out how the Temperature coupling works
If I understood correctly this implements the Berendsen Bath (in NAMD user’s guide is quoted X-PLOR user’s guide, which, in turn, quotes Berendsen). The Berendsen bath, however, requires a time constant; something like
langevinDamping $gamma ;# damping coefficient [1/ps]
but for the Berendsen bath instead of the Langevin dynamics. However, I didn’t find any mention of any
or something similar in NAMD user’s guide. Can somebody explain to me how the whole thing works?
PS: Last question it is possible to implement Nose’-Hoover thermostats in NAMD?
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