[gmx-users] Per atom energies

[Mark Abraham]

Hi,

On Sat., 28 Mar. 2020, 04:04 Guilherme Carneiro Queiroz da Silva, <
gcarneiroq at 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<http://www.mdstress.org/index.php/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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