[gmx-users] pressure coupling
mark.j.abraham at gmail.com
Tue Jan 2 06:57:41 CET 2018
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't know what I
> should do I thought pressure must converge to 1 bar exactly and 1.5
> isn't appropriate
> I get this pressure in after NPT step and I worried it'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'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.
> Excuse me for the rudimentary quetion.
> Thank you very much
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