On 10/2/12 5:20 AM, Anik Sen wrote:
Hi everybody,
I am still in confusion in which thermostat my be good for
NPT MD calcualtions with protein and DNA. V-rescale, berenseden, Nose-hoover;
parinello-rahman thermostats. Is the temperature and pressure coupling will be
similar or different.
The different algorithms will lead to different distributions for temperature
and pressure values. What does your reading of the primary literature for these
algorithms tell you? What methods do others use when simulating similar
systems? What does your searching of the list archive turn up? Hint: we
discuss this type of thing a lot, so there's plenty in the archive from which to
learn.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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