----- Original Message ----- From: ms <deviceran...@gmail.com> Date: Monday, August 30, 2010 10:15 Subject: Re: [gmx-users] Re: NPT simulation To: jalem...@vt.edu, Discussion list for GROMACS users <gmx-users@gromacs.org>
> On 29/08/10 19:39, Justin A. Lemkul wrote: > > >When dividing the energy of a system by the number of molecules > (in a > >homogeneous system), you are extracting what I believe is commonly > >referred to as "configurational energy" which, for relatively simple > >systems, should converge fairly quickly. The reason your total energy > >values increase with system size is a simple matter of > potential energy. > >More interactions mean that the magnitude of the potential will > >increase, and likewise with the kinetic energy, more particles > that have > >velocity imply a greater sum. > > > >You can convince yourself of this fact by running relatively short > >simulations of water boxes, using, i.e. spc216.gro and then a larger > >construct from it. Within a few hundred ps, you should get reasonably > >converged configurational energies, though of course the total energy > >will be larger simply by virtue of the system size. > > > >Energies are in kJ/mol, no question. The extrapolation would be > that a > >mole of a given species in the given configuration would have this > >energy in kJ. For a single molecule, the energy is whatever > value you > >obtain divided by Avogadro's number, which is a relatively > unimportant>quantity if you are interested in bulk dynamics. > > Wait, now I am confused too. > I always understood that energy was meant as kJ/mol for a mol of > my *system*, that is, if I have a box with 10 identical > molecules, then I g_energy gives me out the energies of that *box*. Yes, that's right. I don't think Justin contradicted that statement. Expressing energies in kJ/mol is just a convenience. It does not imply size independence - see my earlier post. Mark
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