AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Sep 08 2008 - 13:51:49 CDT

yes perhaps I implied the wrong thing by trying to explain the general
purpose of intensive energy units. for our systems, of cousre the
results will depend on the # of molecules, we're giving energies in
per mole of systems, not really dividing out to the molecule. it just
really wasn't clear what the question was, and whether it was general
about why one uses per-mole units, or something specific about Amber
implementation.

On Mon, Sep 8, 2008 at 3:02 PM, Marek Malý <maly_at_sci.ujep.cz> wrote:
> Dear Carlos,
>
> if I understood well (and seems to me that Prof. Case confirmed that yes),
> your sentence
>
> "...that is that the energy reported does not depend on how
>>
>> many molecules you are measuring/simulating."
>
> is not probably valid.
>
> It means that if I simulate for simplicity N1 molecules of H2O with the
> total energy of this system E1[kcal/mol] and
> than I simulate N2 molecules of H2O (under the same physical conditions like
> in first case) with the total energy
> E2[kcal/mol] than if N1 is different from N2 than also E1 will be different
> from E2.
> In other words reported numbers E1,E2 are not energies of one mol of H2O in
> given conditions but:
>
> E1 = energy of N1 x NA molecules = N1 moles of H2O measured in [kcal]
> E2 = energy of N2 x NA molecules = N2 moles of H2O measured in [kcal]
>
> This conclusion should be OK if the results from previous communication is
> OK.
> Also my experiences agree with the conclusion that we should think about one
> mole
> of "whole systems" and not about one mole of molecules when we would like
> interpret
> unit [kcal/mol].
>
> So I think this is probably different for example from the molar heat
> capacity of water which
> really gives me the heat which is necessary to add to one mole of H2O
> molecules to cause increase
> 1K in temperature.
>
> The hypothesis that we should think about energy one mole of "whole systems"
> not about mole of
> some subunits i.e. "molecules" in interpretation of [kcal/mol] unit is clear
> also from the fact, that in practice we are often dealing
> with heterogenous, complex systems where you can not say: "This system is
> composed of N of one type molecules, hence is resonable to deal
> with energy of one mole of this molecules in given conditions."
>
> Here:
>
> http://physics.ujep.cz/~mmaly/UnitDiscussion/
>
> are results from 3 simulations of H2O in Materials Studio. All under the
> same conditions.
> There are 3 cases: 100,200,300 molecules of H2O. It is pretty seen that the
> energies
> measured in [kcal/mol] are in all three cases different.
>
> I think that similar results (at least qualitatively) gives us calculation
> of the same
> systems in Amber.
>
> Marek
>
>
>
>
>
>
> Dne Mon, 08 Sep 2008 16:56:48 +0200 Carlos Simmerling
> <carlos.simmerling_at_gmail.com> napsal/-a:
>
>> 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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>>>
>>>
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>
>
>
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