[gmx-users] potential energy of a system
mukherjee.saumyak50 at gmail.com
Wed Mar 29 17:04:27 CEST 2017
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:
>> 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
>> 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 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
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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
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