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 <fpoosa...@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.abra...@gmail.com> > wrote: > > > Hi, > > > > On Sun, Nov 26, 2017 at 6:35 PM Faezeh Pousaneh <fpoosa...@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.abra...@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 < > fpoosa...@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.abra...@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 <fpoosa...@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 > > > > > > > -- > > > > > > > Gromacs Users mailing list > > > > > > > > > > > > > > * Please search the archive at > > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > > before > > > > > > > posting! > > > > > > > > > > > > > > * Can't post? 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