AMBER Archive (2008)

Subject: Re: AMBER: Explanation of the energy unit ?

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Sep 08 2008 - 09:56:48 CDT

your questions aren't quite clear, but if you mean why are the units
in per mole, it's because it is much easier (both in experiment and
computation) to deal with units that are intensive rather than
extensive, that is that the energy reported does not depend on how
many molecules you are measuring/simulating.

On Mon, Sep 8, 2008 at 11:01 AM, Marek Malý <maly_at_sci.ujep.cz> wrote:
> Dear Prof. Case,
>
> thank you very much for your answer which
> made me sure that my interpretation of
> the [kcal/mol] unit is OK.
>
> The second part of my question:
>
> "The sense (background) of this "strange" unit" is unfortunately still
> nonanswered.
>
> I have to say that in relevant Wikipedia page:
>
>
> http://en.wikipedia.org/wiki/Units_of_energy
>
>
> is zero information about this unit which is very strange to me
> since in computational(and probably not only computational) chemistry is
> this (at least it seems to me)
> energy unit standard. So maybe it would be worth to spend some time
> to amend information about this unit in above Wikipedia page include the
> right
> interpretation and some background. Of course I do not mean that it is task
> for you
> personally :)), but for anybody who knows the right answers.
>
> I think that could be interesting to answer question:
> "What was the reason for introducing energy unit which gives me energy of NA
> my systems in [kcal] or in another
> words what was the reason to introduce energy unit which is NA times smaller
> than [kcal] ?"
>
> Is it because the relevant energies expressed using this small unit are
> usually "nice" numbers like 30.56, 400.78 and
> not numbers like 30.56 * 10^-n ... which should appear using any other
> energetical unit or is there some
> deeper background ? I think that there should be some deeper background
> since there is use precisely Avogadro
> constant in relationship with [kcal].
>
>
> Marek
>
>
>
>
> Dne Mon, 08 Sep 2008 00:12:22 +0200 David A. Case <case_at_biomaps.rutgers.edu>
> napsal/-a:
>
>> On Sat, Sep 06, 2008, Marek Malý wrote:
>>>
>>> Let's assume that we have some molecular system Y and we for example
>>> calculate the total energy of this system. Lets say that result is
>>> X[kcal/mol].
>>>
>>> My only interpretation is that X is the energy in [kcal] of NA systems
>>> Y.
>>> So if I want energy of one system Y in [kcal] it is X/NA. Where NA is
>>> Avogadro constant.
>>
>> This is correct. 1 cal = 4.184 J (exactly). See wikipedia (or other
>> places) for a discussion of its history and use.
>>
>> ...dac
>>
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