[gmx-users] multicomponent system- units

Mark Abraham Mark.Abraham at anu.edu.au
Tue Apr 12 06:10:04 CEST 2011

> Hello Mark,
> Thank you for your reply. I have already created the energy groups. I 
> am trying to validate pairwise energy values (nonbonded) with some 
> other work ( a thermodynamic model) where they fit these AA AB BB 
> (E_AA, E_AB, E_BB) energies so that some phase diagrams are 
> reproduced. The pairwise energies defined in the model are in KJ/mol.

So how did they compute these interaction energies?

The energy quantity GROMACS reports for a microstate can be best thought 
of as the energy one would have for a mole of such microstates. 
Alternatively, divide by N_A and that's the energy for this microstate - 
but that's a much less convenient number to use.

To obtain a quantity that is independent of the number of particles, you 
have to normalize for the number of interactions of each type. If these 
are all pairwise between atoms in a unary system, then you need to 
divide by the square of the number of atoms. So for the mixed 
interaction energy of the binary system, you divide by the product of 
the respective numbers of atoms.

You should also verify that these actually are converged observables 
that are independent of the number of particles by simulating replicates 
from different starting configurations, and systems of different sizes.


> Since my energies are not per mol, my results are useless, 
> unfortunately. As they depend on number of molecules in the system. To 
> achieve my goal, what do you suggest? For a binary system, can I run 
> two separate simulations for pure A and B in which case using -nmol 
> gives per mol energies and somehow predict AB from them? Does this 
> make sense?
> Please guide me, I am stuck on this..
> Thanks,
> On 9 April 2011 20:56, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>     On 8/04/2011 12:18 PM, Elisabeth wrote:
>         Hello everyone,
>         I have encountered a simple problem. For a homogenous system
>         what g_energy reports is dependent on the system size and one
>         needs to use -nmol option to divide energies by number of
>         molecules to obtain per mol values.
>         I am attempting to extract interaction energies between
>         species in a three component system. I am puzzled how this can
>         be achieved for such a system. Say there are 100 solvent, 20
>         solute A and 10 B molecules.
>     You would have to start by defining energy groups that contain
>     relevant sets of molecules (see manual). Even once you've got
>     them, the group-wise energies won't mean much of anything. Every
>     observable is dependent on the configuration microstate, and
>     unless you can estimate the relative population of different
>     microstates to estimate a free energy...
>     Mark
>     -- 
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