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.
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? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at http://www.gromacs.org/ > > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
