[gmx-users] Pressure Question

[Téletchéa Stéphane]

Le 06/11/2014 06:16, Antonio Baptista a écrit :
>
> In particular, the virial-based "instantaneous pressure" (call it P') 
> computed in simulations has its ensemble average equal to the 
> thermodynamic pressure P (check any good book on molecular 
> simulation). But, as others already pointed out, this P' is well-known 
> to show extremelly large fluctuations, meaning that its average 
> computed from the simulation has usually a very large statistical 
> spread. In other words, although the ensemble average of P' is 
> strictly equal to P, its simulation average is a random variable that 
> often shows large deviations from P (especially for short 
> simulations). To get an idea of what is an acceptable error for the 
> average of P', you may look at its distribution histogram in the NPT 
> simulation. 

Dear Antonio,

Sorry if my message sound "aggressive" when I talked about "totally 
irrevelevant", I will clarify my thoughts.

 From a theoretical point of view, you are right, each ensemble is 
accessible.

 From a biological point of view, though, the concept of fixing the 
volume is less reasonable:
we live at constant pressure and temperature, and also at tighly 
controlled pH, and salt concentrations.

The volume varies though, as you feel it when the weather is getting hot 
or cold.

My point was exactly what your are telling in a more formal way than me:
"this P' is well-known to show extremely large fluctuations"

Well, digging a bit more on my "feeling", I also found opposite 
arguments on the AMBER mailing list,
like here: http://archive.ambermd.org/201103/0431.html

So I'll got back again on my research and adjust my "mind" on the actual 
bleeding edge simulations
taking into account all the recent code and force fields progresses.

Best,

Stéphane

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