Hi Marek,
Carlos point is indeed valid. What you are missing here is that the
results you get are for one mole *of your system*, whatever it is. If
you system has N1 molecules of water, then the results in kcal/mol
mean y kcal in 1 mole * N1 molecules of water. Obviously, the results
from a different number of water molecules in your system will have to
be different. Of course, then, E1/N1 should be approximately equal to
E2/N2, and that's what your results show.
(
http://physics.ujep.cz/~mmaly/UnitDiscussion/)
Gustavo.
On Mon, Sep 8, 2008 at 3:02 PM, Marek Malư <maly.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.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 Malư <maly.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.biomaps.rutgers.edu>
>>> napsal/-a:
>>>
>>>> On Sat, Sep 06, 2008, Marek Malư 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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Received on Wed Sep 10 2008 - 06:07:29 PDT
