[gmx-users] Regarding -nmol option

Justin Lemkul jalemkul at vt.edu
Fri Jun 22 16:08:02 CEST 2018

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 A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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