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

[Faezeh Pousaneh]

Please note that the carbon is a virtual site, so has not mass. So the DOF
does not influence of its configurations on average. Besides the angle   of
M--C--M is always 180.

Mark, I compare the results of average distributions not a snapshot.

Justin, the only LJ are from atom C with next molecules in both systems.
(In fact I got the idea from your carbon dioxide tutorial, in which later I
will add two more virtual sites with charges to create a dipole moment for
my atom (e.g C here), but first I must understand this stage)



Best regards


On Sun, Nov 26, 2017 at 7:12 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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