On Thu, 6 Nov 2014, Téletchéa Stéphane wrote:
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.
No problem, Stéphane. I was just trying to avoid propagating the wrong
idea that a parameter is irrelevant in an ensemble where its value is not
explicitly imposed, an idea I saw stated before in several discussions.
Anyway, it seems I misunderstood you, since you say you were actually
making the same point... :)
Best,
Antonio
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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