[gmx-users] nrexcl=3: ambiguous?
mark.j.abraham at gmail.com
Mon Feb 19 08:52:09 CET 2018
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.
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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