[gmx-users] pressure coupling

[Mark Abraham]

Hi,

On Mon, Jan 1, 2018 at 7:43 AM <kordzadeh at aut.ac.ir> wrote:

> Hello Dr.Lemkul
>
> Thank you very much for your help and your answer
>
> my average pessure is 1.5 bar and it fluctuates + and - 295 bar .
>
> as your guide, I will consider it near to 1 bar. I didn&#39;t know what I
> should do I thought pressure must converge to 1 bar exactly and 1.5
> isn&#39;t appropriate
>
> I get this pressure in after NPT step and I worried it&#39;s value of
> pressure changes and effects my results in production run.
>

Pressure fluctuates according to the current movement of the particles.
Stop thinking about it as a fixed quantity. Some background reading about
statistical mechanics may help :-)


> Time of NPT step was 8.5 ns, I get this optimized time after 40 runs and
> this procedure is very time consuming.
>
> I think I became too sensitive about pressure coupling. what is the
> acceptable deviation range?
>
> should I select a optimize time for md (production run) that pressure is
> approximately near to 1 bar or time of production run isn&#39;t important?
>

If you are going to simulate in NPT, then pressure will still fluctuate.
Pick a time after the volume or density have converged, which is easier to
see, because the fluctuations are much lower.


> In lysozyme tutorial in figure of pressure , there is a red line for
> average pressure, how does that line obtain?
>

It's surely an average from gmx energy. You have one, too.

Mark


> Excuse me for the rudimentary quetion.
>
> Thank you very much
>
> Regards
>
> Azadeh
>
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