On Wed, Jan 22, 2014 at 3:53 AM, Zhuang, Yu <yu.zhuang.tum.de> wrote:
> Hallo,
> currently I am doing a set of MD for protein under constant pressure (150
> bar). However, the results shows that the pressure of MD system experiences
> some fluctuation, which look crazy somehow. Might anyone has an idea for
> this situation?
>
> For example:
> NSTEP = 469000 TIME(PS) = 1234.500 TEMP(K) = 291.72 PRESS =
> 26.8
> NSTEP = 481000 TIME(PS) = 1240.500 TEMP(K) = 292.65 PRESS =
> -72.1
> NSTEP = 565000 TIME(PS) = 1282.500 TEMP(K) = 292.34 PRESS =
> 187.3
> etc.
>
This is perfectly normal. The reason this happens is because water is
virtually incompressible. Tiny changes in the system volume yields large
differences in pressure. The average pressure will come out about right
(although you have to run for a LONG time to get the standard deviation
lower than the target pressure itself).
The metric you should monitor is the system density, since that is far less
sensitive to small changes in volume. With a pressure of 150 bar instead
of standard atmospheric pressure around 1 bar, you should expect an
increase in system density compared to the one you get at 1 bar. However,
given water's very small isothermal compressibility, I would expect the
density increase to be quite small.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Jan 22 2014 - 07:00:02 PST
