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

[Mark Abraham]

Hi,

Your linear version has two rotation axes (and thus DOF) because it has
mass distribution. Your point version has no mass distribution.

Mark

On Sun, Nov 26, 2017 at 7:52 PM Faezeh Pousaneh <fpoosaneh at gmail.com> wrote:

> 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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