[gmx-users] Regarding -nmol option
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
> 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.
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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