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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