[gmx-users] Pressure

[Frederic Leroy]

Joanne Hanna wrote:

>Hi 
>I am doing and NVT of a solvated enzyme and examples of my pressure are:
>
>
>Step           Time         Lambda
>  16        0.03200        0.00000
>Pressure (bar)
>    4.49377e+02
>
>Step           Time         Lambda
>  17        0.03400        0.00000
>Pressure (bar)
>4.36604e+02
>
>Step           Time         Lambda
>  18        0.03600        0.00000
>Pressure (bar)
>4.77199e+02
>
>Aren't these pressures way too high and if so how do i fox this, sorry
>if this is a very silly question, I am quite new to MD.
>
>Jo 
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Hi Jo,

well, you'll learn that the pressure is somewhat difficult to calculate 
using MD and you will most of the time observe huge fluctuations of this 
quantity so that the statistical error on its averaged value wouldn't 
help you very much.
You should better concentrate on  the density of your system. You should 
equilibrate it using the barostat at the pressure you would like and run 
the calculations a time long enough so that your density would converge, 
i.e. fluctuates around a plateau. Then the pressure you would like 
should be correct but you won't see it numerically because of the 
fluctuations.
In other words, if the initial configuration of your system is dilute, 
then, running an NPT calculation at a sufficiently high pressure will 
increase the density of the system up to its equilibrium value at this 
expected pressure.

'hope 't will help.

Frederic, Tarragone U., Spain.