[gmx-users] Regarding -nmol option

[Justin Lemkul]

On 6/22/18 3:19 AM, Apramita Chand wrote:
> Dear All,
> In computing interaction energies between groups from g_energy, the -nmol
> option needs an integer argument that ( as mentioned)  should be equal to
> total no of particles in the system.

The -nmol option should be set to the number of *molecules* (not 
particles) in a pure liquid when computing the thermodynamic properties 
listed in the table to which that statement refers.

> So if I have a protein-urea-water solution of a single protein, 15 urea and
> 984 water molecules, for protein-urea interaction energy, what should -nmol
> be?
> No.of protein+urea molecules?
> Or total number of molecules, including water??
>
> Again for protein-water interaction energies, -nmol should be protein+
> water molecules or total number of molecules?

The option is not really relevant here. If you're computing urea-protein 
interaction energy, you could convert the quantity to a per-molecule 
interaction energy simply by dividing by 15.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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