Re: [h5md-user] Volume

[Pierre de Buyl]

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