[gmx-users] Pressure Question
baptista at itqb.unl.pt
Fri Nov 7 03:59:11 CET 2014
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
> 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... :)
> 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
> 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.
> Team Protein Design In Silico
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