AMBER Archive (2008)

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

From: Marek Malý (maly_at_sci.ujep.cz)
Date: Mon Sep 08 2008 - 14:02:37 CDT

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
>>>
>>> -----------------------------------------------------------------------
>>> The AMBER Mail Reflector
>>> To post, send mail to amber_at_scripps.edu
>>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>>> to majordomo_at_scripps.edu
>>>
>>> __________ Informace od NOD32 3424 (20080907) __________
>>>
>>> Tato zprava byla proverena antivirovym systemem NOD32.
>>> http://www.nod32.cz
>>>
>>>
>>
>>
>>
>> --
>> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
>> http://www.opera.com/mail/
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo_at_scripps.edu
>>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>
> __________ Informace od NOD32 3426 (20080908) __________
>
> Tato zprava byla proverena antivirovym systemem NOD32.
> http://www.nod32.cz
>
> 

-- 
Tato zpráva byla vytvořena převratným poštovním klientem Opery:  
http://www.opera.com/mail/
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu