[gmx-users] Test particle insertion change in energy - group cut off scheme

[Arun Srikanth]

Thank you.

Can you please elaborate on this or clarify the following questions?

1. Supposing I have inserted one water molecule inside a polymer (an
interconnected network with net zero charge),

the electrostatic interactions should be computed between every atom of
water and  polymer atoms within a cutoff distance and use per atom
ewald summation due to long-range nature of electrostatics.

I believe if one chooses group cutoff the interactions are based on centre
of mass of charged groups ?.

Also not clear how gromacs will handle charged group in this particular
case since I have interconnected (crosslinked) network and not a fixed
number of monomers in which case the all the atoms belonging to one monomer
can be considered a charged group.



Thank you again
Arun



On Sat, Mar 3, 2018 at 5:44 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> TPI will only work if you choose the group cutoff scheme. But the impact of
> that difference is nearly zero.
>
> Mark
>
> On Sat, Mar 3, 2018, 22:29 Arun Srikanth <askforarun at gmail.com> wrote:
>
> > Hello all
> >
> > I was going through tpi.cpp file in the latest version of gromacs.
> >
> > I found this flag
> >
> > "TPI does not work (yet) with the Verlet cut-off scheme"
> >
> > My question:
> >
> > Does test particle insertion use the group cut off scheme to calculate
> the
> > change in energy ? (assuming equilibrium trajectories generated using
> > verlet cutoff)
> >
> > Thank you
> > Arun
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