[gmx-users] Energy group exclusions

Mark Abraham mark.j.abraham at gmail.com
Thu Dec 15 22:39:59 CET 2016


As you've seen in
such exclusions are only for efficiency, which would make negligible impact
here. And anyway the bonds in your molecule probably generate nonbonded
exclusions within that molecule from the nrexcl moleculetype setting.


On Thu, 15 Dec 2016 17:11 #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg> wrote:

> Dear all,
> I have a system containing one charged molecule in bulk water and I have
> frozen the molecule at the centre of the box. I run energy minimization
> followed by equilibration by NPT for 100ps and finally NVT production run.
> I wanted to know if it is needed to use energy group exclusions as my
> system has only only frozen molecule so there won't be any atom - atom non
> bonded interaction anyways between 2 frozen atoms, however within this
> molecule I have 3 atoms, so will their non bonded interaction also cause
> unrealistic energy values?
> Thanks
> Sukriti Gupta
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