[gmx-users] Electron density using g_density

Justin Lemkul jalemkul at vt.edu
Tue Jan 16 17:42:52 CET 2018

On 1/16/18 11:37 AM, Mohsen Ramezanpour wrote:
> Dear Gromacs users,
> In the man page of g_density for calculation of electron density, it is
> mentioned that:
> "The number of electrons for each atom is modified by its atomic partial
> charge."
> https://linux.die.net/man/1/g_density
> In some publications, it seems the authors just took the atomic number as
> the number of electrons for each atom name.
> For instance, for POPC: they took N=7, P=15, O=8, C=6, and H=1
> In some others, they did not consider the partial charge.
> For instance, for POPC: they took N = 6, P = 16 and all the O atoms = 8,
> C=6, and H=1
> So, I was wondering which approach do you think is better?
> Will the difference between these approaches matter for making conclusions?

The code accounts for the partial charges (see calc_electron_density() 
in gmx_density.cpp). You should specify the number of electrons on the 
elemental form of the atom. One cannot ascribe the entire +1 charge to N 
or -1 to P, anyway, so that's a false approach.



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

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340 West Campus Dr.
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