[gmx-users] Please help

[Justin Lemkul]

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

-- 
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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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