[gmx-users] Electron density using g_density
ramezanpour.mohsen at gmail.com
Tue Jan 16 18:16:13 CET 2018
I will as you recommended.
The last approach was described in a book chapter for bilayer simulation.
I had difficulty to justify that approach.
On Tue, Jan 16, 2018 at 9:42 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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
> 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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