Re: [gmx-users] Per atom energies

[David van der Spoel]

Den 2020-03-28 kl. 04:01, skrev Guilherme Carneiro Queiroz da Silva:

Hi all,

I look on google for any answers for such question in this maillist, and I 
found related questions but no final answer.

I wish to compute the heat flux for my system using GK relations. I found the 
gromacs extension force the calculation of the per atom stress 
(http://www.mdstress.org/index.php/mdstresslib/). However, it still lacks the 
per atom energies. Did someone manage to extract such properties?

I'm aware i could use enemat but had to do a large numbers of reruns in order 
to cover each atom obeying the group limit of gromacs, since this could be 
tedious I'm looking for other solutions. Could editing the trajectory code in 
order to extract not only forces but also the energies be the only solution?



The reason that there is no support is that it is not physically 
meaningful, at least not to my knowledge. How would you partition the 
bond energy in a HCl molecule into atoms?


In an isolated system it is in principle possible to compute interaction 
energies, using the typical pair potentials that classical force fields 
apply. However, these force fields ignore higher order interactions, 
which means this is a crude approximation.


In a periodic system the computation of energies and energy components 
is even more cumbersome, although we have attempted that using potential 
of mean force calculation in JCTC 9 pp. 4542-4551 (2013).




Thanks for any help,

Guilherme Carneiro


mdStress.org :: MDStressLib
MDStress Library. MDStressLib is a standalone C++ library developed for local 
stress calculations. This library can be integrated into any molecular 
simulation code to compute local stress fields in 3D.
www.mdstress.org




--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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Re: [gmx-users] Per atom energies

[Mark Abraham]

Hi,

On Sat., 28 Mar. 2020, 04:04 Guilherme Carneiro Queiroz da Silva, <
gcarnei...@pos.iq.ufrj.br> wrote:

> Hi all,
>
> I look on google for any answers for such question in this maillist, and I
> found related questions but no final answer.
>
> I wish to compute the heat flux for my system using GK relations. I found
> the gromacs extension force the calculation of the per atom stress (
> http://www.mdstress.org/index.php/mdstresslib/). However, it still lacks
> the per atom energies. Did someone manage to extract such properties?
>
> I'm aware i could use enemat but had to do a large numbers of reruns in
> order to cover each atom obeying the group limit of gromacs, since this
> could be tedious I'm looking for other solutions. Could editing the
> trajectory code in order to extract not only forces but also the energies
> be the only solution?
>

The energies are computed as a sum over interactions and saved only in
aggregate. There's no support for anything more useful than reruns with
energy groups.

Mark

Thanks for any help,
>
> Guilherme Carneiro
>
>
> mdStress.org :: MDStressLib >
> MDStress Library. MDStressLib is a standalone C++ library developed for
> local stress calculations. This library can be integrated into any
> molecular simulation code to compute local stress fields in 3D.
> www.mdstress.org
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Per atom energies

[Guilherme Carneiro Queiroz da Silva]

Hi all,

I look on google for any answers for such question in this maillist, and I 
found related questions but no final answer.

I wish to compute the heat flux for my system using GK relations. I found the 
gromacs extension force the calculation of the per atom stress 
(http://www.mdstress.org/index.php/mdstresslib/). However, it still lacks the 
per atom energies. Did someone manage to extract such properties?

I'm aware i could use enemat but had to do a large numbers of reruns in order 
to cover each atom obeying the group limit of gromacs, since this could be 
tedious I'm looking for other solutions. Could editing the trajectory code in 
order to extract not only forces but also the energies be the only solution?

Thanks for any help,

Guilherme Carneiro


mdStress.org :: MDStressLib
MDStress Library. MDStressLib is a standalone C++ library developed for local 
stress calculations. This library can be integrated into any molecular 
simulation code to compute local stress fields in 3D.
www.mdstress.org

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