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

[Mark Abraham]

Hi,

Please see the reference manual for details, but the charge groups are
defined in the topology however you wish (and need not have a net charge).

Mark

On Sun, Mar 4, 2018, 00:18 Arun Srikanth <askforarun at gmail.com> wrote:

> 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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