[gmx-users] Doubt regarding nrexcl parameter in topology

[Chandan Choudhury]

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...”*