[gmx-users] nrexcl=3: ambiguous?

[Saumyak Mukherjee]

Thanks Mark for your comments.



‌

On 19 February 2018 at 13:21, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> Hi,
>
> Typically 1-4 interactions are regarded as bonded interactions implementing
> a non-bonded functional form. So a request to exclude non-bonded
> interactions between atoms connected by adjacent bonds does not apply. The
> requirement for particular kinds of 1-4 interactions are imposed by
> construction of the force field.
>
> Mark
>
> On Mon, Feb 19, 2018 at 6:34 AM Saumyak Mukherjee <
> mukherjee.saumyak50 at gmail.com> wrote:
>
> > Dear Users,
> >
> > As mentioned in the manual, *nrexcl = 3* means "*excluding non-bonded
> > interactions between atoms that are no further than 3 bonds away*". This
> > means, as I understand, 1-4 interactions are also excluded.
> >
> > However, after simulation when "gmx energy" is used, it gives output for
> > 1-4 interactions. How is this possible?
> >
> > Any help/suggestion is appreciated.
> >
> > Thanks & regards,
> >
> > *Saumyak Mukherjee*
> >
> > Senior Research Fellow,
> > Prof. Biman Bagchi's Lab,
> > Solid State and Structural Chemistry Unit,
> > Indian Institute of Science,
> > Bangalore - 560012,
> > Karnataka, India.
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-- 
Thanks & regards,

*Saumyak Mukherjee*

Senior Research Fellow,
Prof. Biman Bagchi's Lab,
Solid State and Structural Chemistry Unit,
Indian Institute of Science,
Bangalore - 560012,
Karnataka, India.