[gmx-users] virtual site connected to dummy massive site

[Mark Abraham]

Hi,

On Sun, Nov 26, 2017 at 6:35 PM Faezeh Pousaneh <fpoosaneh at gmail.com> wrote:

> Hi Mark, sorry I am not convinced yet. I hope you did not misunderstand my
> question, I have no charges in systems on any atoms. So the extra DOF do
> not effect on potential.
>

Charge has nothing to do with it. The potential is computed from all the
interactions in the system, which in your case includes LJ. You aren't
going to generate the same ensemble of configurations in your two cases, so
you cannot expect to observe the same distribution of potential energy.

Note that it would have been nice to say whether you were comparing a
distribution of energies or a snapshot. As it is, we are guessing.

Mark

Best regards
>
>
> On Fri, Nov 24, 2017 at 11:03 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > Potential energy is a function of configuration. You can expect the same
> LJ
> > energy if you compare the same configuration, ie that the distribution of
> > states is identical. But if you would have the same total energy and a
> > different distribution between PE and KE (because the DOF change) then
> you
> > will not sample the same states.
> >
> > Mark
> >
> > On Fri, Nov 24, 2017 at 10:56 AM Faezeh Pousaneh <fpoosaneh at gmail.com>
> > wrote:
> >
> > > Dear Mark,
> > > thanks, but degrees of freedom goes to kinetic energies, still LJ
> > energies
> > > must be the same, yes?
> > >
> > >
> > > Best regards
> > >
> > >
> > > On Fri, Nov 24, 2017 at 8:22 AM, Mark Abraham <
> mark.j.abraham at gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > Your systems have different available degrees of freedom, so they
> > sample
> > > > difference spaces. The energies you observe reflect that difference.
> > > >
> > > > Mark
> > > >
> > > > On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh <fpoosaneh at gmail.com>
> wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > I have a system containing of a virtual site of carbon connected
> > > > > symmetrically to two dummy massive sites (no charge). like :
> > M---C---M
> > > > > My problem is the results I get from simulation of this system is
> not
> > > > equal
> > > > > with results of single Carbon system simulation with mass of 2M (at
> > > > exactly
> > > > > similar conditions)?
> > > > > They produce different LJ coul energies, I have even tried for
> > > > non-charged
> > > > > systems.
> > > > >
> > > > > Thank you in advance for help,
> > > > > Best regards
> > > > > --
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