[gmx-users] Doubt regarding nrexcl parameter in topology

[bipin singh]

Thank you Chandan for your reply and explanation.


------------------------------
Thanks and Regards,
Bipin Singh

On Sat, Jan 17, 2015 at 11:53 AM, Chandan Choudhury <iitdckc at gmail.com>
wrote:

> Dear Bipin,
>
> With nrexcl = 3 it excludes neighbours 3 bonds away, in this case your (ii)
> option falls.
> But an extra LJ and electrostatic interactions, is added between 1-4 pairs,
> if gen-pair is yes for the force field.
> These interactions are scaled by their respective fudge factor.
> For gromos ff, the gen-pair is no. Thus there are no extra LJ or
> electrostatics. 1-4 pair contributes to the potential energy
> only through dihedrals.
>
> Chandan
>
>
> On Sat, Jan 17, 2015 at 7:42 AM, bipin singh <bipinelmat at gmail.com> wrote:
>
> > Dear All,
> >
> > I have a doubt regarding the definition of nrexcl parameter in topology
> of
> > a molecule (Gromos force field)
> >
> >
> > As mebtioned in the Gromacs manual, nrexcl = 3 stands for excluding
> > non-bonded interactions between atoms that are no further than 3 bonds
> > away, so does it mean that:
> >
> >
> > (i) Exclude the 1-2 and 1-3 pairs and but not the 1-4 pair.
> >
> >  OR
> >
> > (ii) Exclude the 1-2, 1-3 and the 1-4 pairs.
> >
> >
> > Thanks and Regards
> > Bipin
> > --
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>
> --
>
> --
> Chandan Kumar Choudhury
> National Chemical Laboratory, Pune
> India
>
> *"All work and no play makes Jack a dull boy...”*
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