[gmx-users] Re: NPT simulation

Mark Abraham mark.abraham at anu.edu.au
Mon Aug 30 02:23:35 CEST 2010

----- Original Message -----
From: ms <devicerandom at gmail.com>
Date: Monday, August 30, 2010 10:15
Subject: Re: [gmx-users] Re: NPT simulation
To: jalemkul at vt.edu, Discussion list for GROMACS users <gmx-users at 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.


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