[gmx-users] multicomponent system- units

Elisabeth katesedate at gmail.com
Tue Apr 12 05:39:28 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.

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..


On 9 April 2011 20:56, Mark Abraham <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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