[gmx-users] nrexcl=3: ambiguous?
mukherjee.saumyak50 at gmail.com
Mon Feb 19 11:44:38 CET 2018
Thanks Mark for your comments.
On 19 February 2018 at 13:21, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 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.
> > --
> > 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
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.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
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
Thanks & regards,
Senior Research Fellow,
Prof. Biman Bagchi's Lab,
Solid State and Structural Chemistry Unit,
Indian Institute of Science,
Bangalore - 560012,
More information about the gromacs.org_gmx-users