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

[Mark Abraham]

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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