[gmx-users] multicomponent system- units

[Mark Abraham]

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