[gmx-users] Energy units

[Tsjerk Wassenaar]

Hi,

I think that the best interpretation is that the energy is given as kJ
per mole of simulation systems :)

Cheers,

Tsjerk

On Thu, Jan 7, 2010 at 8:42 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Cheong Wee Loong, Daniel wrote:
>>
>> Thanks Mark for your reply.
>>
>> So if I understand you correctly, it's not really a mole of anything in
>> particular, it's just an energy value divided by Avogadro's number, and this
>> happens to be consistent with the forcefield parameters as well.  So if you
>> have just a single molecule, that energy value is still divided by
>> Avogadro's number.
>>
>> So if I were to take an interaction energy per unit area to estimate an
>> interfacial energy, and I want to relate this to an experimental value given
>> in dynes/cm, I would just need to multiply by Avogadro's number, in addition
>> to all the other unit conversions (kJ/nm2 to dynes/cm), for the units to be
>> consistent.  Am I correct in my understanding?
>
> I think so. Whether such a quantity can be measured with an MM force field
> might be another matter!
>
> Mark
>
>> -----Original Message-----
>> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
>> On Behalf Of Mark Abraham
>> Sent: Thursday, January 07, 2010 3:03 PM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] Energy units
>>
>> Cheong Wee Loong, Daniel wrote:
>>>
>>> Hi all,
>>>
>>>
>>>
>>> This may be a silly and trivial question, but the energy unit given in
>>> Gromacs is kJ/mol.  What I don't quite understand is, the energy is per
>>> mole of what exactly?
>>
>> In a very real sense, it doesn't matter. It's just a label for a
>> convenient bucket of energy for chemistry.
>>
>> The energy of an isolated water molecule has a certain value, which we
>> might measure in joules relative to some defined zero. Two such
>> molecules at infinite separation would have twice that energy, etc. Once
>> we start approaching Avogadro's number, we would prefer to express that
>> energy as kJ/mol just for our numerical convenience.
>>
>> Equally, we could take a water molecule and a methane molecule at
>> infinite separation, and add their energy... and add lots more... and
>> get irritated at the size of the number, and just divide by Avogadro for
>> convenience. The system is no longer homogeneous, but so long as we
>> compare energies formed in the same way, our conclusions will be valid.
>>
>> MD force fields are typically parameterized against things like
>> experimental or computational enthalpies of formation, normally measured
>> in kJ/mol (unless you're a unlucky enough to be American!). So the
>> parameters that get derived are conveniently measured in units derived
>> from kJ/mol. We could convert them to "absolute" joules, but the numbers
>> would all be stupid. There's a reason quantum chemists work in Hartrees!
>> Were we to work in absolute joules, the numbers we'd produce then would
>> still relate to the numbers we actually produce in kJ/mol - by Avogadro.
>>
>> Mark
>>
>>> The energy is system size dependent, so if I double the number of
>>> molecules, the energy will double accordingly.  But then the unit kJ/mol
>>> seems to imply that it is size-independent.  So how do I reconcile this?
>>>
>>>
>>>
>>> Also, let's say I have a protein molecule surrounded by water
>>> molecules.  Again in this case, I don't quite understand what "per mole"
>>> means in this case.
>>>
>>>
>>>
>>> Thanks in advance for any insights you can teach me.
>>>
>>>
>>>
>>> Daniel
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist