[gmx-users] Re: NPT simulation
Justin A. Lemkul
jalemkul at vt.edu
Mon Aug 30 02:19:45 CEST 2010
> 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*.
> Is it wrong?
No, exactly as I have explained in the follow-up message to this post. I was
trying to tie this concept into the OP's original observations and attempts to
quantify his results with respect to energetics of individual molecules.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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