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

[Arun Srikanth]

I see. Thank you.  I understand how tpi in gromacs works now. Perhaps my
last question.


Is there a restriction on the number of charge groups in gromacs ?. For
example can it be equal to the number of atoms in the system ?

How do think it will affect the performance of tpi which uses the group cut
off scheme ?

Thank you again
Arun

On Sat, Mar 3, 2018 at 9:44 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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