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Re: [h5md-user] Volume
From: |
Pierre de Buyl |
Subject: |
Re: [h5md-user] Volume |
Date: |
Fri, 8 Nov 2013 09:13:36 +0100 |
User-agent: |
Mutt/1.5.21 (2010-09-15) |
On Fri, Nov 08, 2013 at 08:04:21AM +0100, Konrad Hinsen wrote:
> Pierre de Buyl writes:
>
> > The problem is that, when we are pushing the boundaries of science [1], we
> find
> > ourselves in situations where we cannot convert everything (semi-open
> systems,
> > subsystems, etc.).
> >
> > I am in favor of not having 'volume' mandatory. And neither 'density'.
>
> +1
>
> I have situations (simulations of proteins in gas phase) where my
> system has an energy and a temperature, but neither volume nor density
> (nor pressure). Whether or not one can use thermodynamics on such
> systems is hotly debated (the keyword to look for is "thermodynamics
> of small systems"). But I don't think a file format should impose a
> particular point of view in this debate.
Hey hey, in some systems you can't even define a temperature :-) [1] (Just self
promotion). Still, 'thermodynamics' is nice and up to the "mandatory" part would
be of use in those situations.
Cheers,
Pierre
[1] http://pre.aps.org/abstract/PRE/v87/i4/e042110