[gmx-users] potential energy of a system

[Saumyak Mukherjee]

Dear Mark and Justin,

Thanks a lot for the information

On 29 March 2017 at 18:33, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/29/17 8:43 AM, Mark Abraham wrote:
>
>> Hi,
>>
>> The total potential energy has everything by definition, so I don't know
>> what you're asking.
>>
>> Additivity of the components of the potential energy is an artefact of the
>> construction of the model physics. While it is true that different
>> physical
>> phenomena underlie some of the components, the parameterization of the
>> force field did not target meaningful decomposition of the potential
>> energy. But you might be able to benefit from fortuitous cancellation
>> effects when comparing such things.
>>
>>
> Nitpick here: in CHARMM (and our polarizable model), we seek to get a
> variety of QM interaction energies explicitly correct (interactions with
> water, ions, other small molecules) so indeed there is some reliability in
> these metrics with CHARMM.  Of course, like all force fields, there is some
> inherent error cancellation but we do make an effort to get all of this
> kind of stuff right. Most other force fields, of course, do not, seeking
> instead to get overall properties correct, leaving the details to be
> debatable.  We try to get it all :)
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
================================
*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukherjee at gmail.com
                                smukherjee at sscu.iisc.ernet.in
================================