From: divya nayar (divya.alchemist_at_gmail.com)
Date: Sat Jan 03 2015 - 08:36:05 CST
I am doing REMD simulation of small peptides in explicit solvent using NAMD
2.9 version. I want to know more about the way NAMD generates temperatures
for replicas. It uses an exponential formula, but I want to know the reason
as to why NAMD uses it. Is there any reference from literature for the same
because I have come across other methods of generating temperatures based
on potential energy distributions of the system which have been described
in literature .
What is the advantage of using exponential distribution of temperatures for
replicas of system?
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