[gmx-users] (no subject)

[João Henriques]

> You need some ions to neutralise the system for long range electrostatics
to work.

This mostly applies to PME. However, because PME is basically *de
facto* nowadays,
it will most likely apply in most situations. However, I recently learned
that PME can also be run with a non-neutral system, as PME will introduce a
neutralizing background charge (and dipole corrections). Here is the
thread:
https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg29536.html

> We usually add more to make the simulation more like the real system
(solution or cell).

Just to be the devil's advocate, I'd say that based on anecdotal evidence
adding salt in a MD simulation of a protein changes make little to no
difference. It doesn't behave as expected, most likely due to poor ion
parametrization and integer charges.

J


On Sun, Jan 21, 2018 at 7:16 AM, <jamesmkrieger at gmail.com> wrote:

> You need some ions to neutralise the system for long range electrostatics
> to work. We usually add more to make the simulation more like the real
> system (solution or cell).
>
> > On Jan 21, 2018, at 1:12 AM, Sankaran SV . <119013033 at sastra.ac.in>
> wrote:
> >
> > Dear all,
> >
> >            I am a beginer. I would like to know the purpose of adding
> ions
> > during the simulation process.
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