Re: [AMBER] fluctuation of pressure during MD

From: Zhuang, Yu <>
Date: Thu, 23 Jan 2014 08:11:58 +0000

Dear Jason,
Thank you for your answer. I will continue the MD and see how density is going.
Best regards,Yu

-----Ursprüngliche Nachricht-----
Von: Jason Swails []
Gesendet: Wednesday, January 22, 2014 4:01 PM
An: AMBER Mailing List
Betreff: Re: [AMBER] fluctuation of pressure during MD

On Wed, Jan 22, 2014 at 3:53 AM, Zhuang, Yu <> 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.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jan 23 2014 - 00:30:03 PST
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