[gmx-users] Re: NPT simulation

Justin A. Lemkul jalemkul at vt.edu
Mon Aug 30 02:19:45 CEST 2010

ms wrote:
> 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.


> m.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list