[gmx-users] Electron density using g_density

[Mohsen Ramezanpour]

Hi Gromacs users,

My system is composed of three lipid molecules.
When I made the topology file for new lipids in the system, I chose some
atom names by my choice.
Now, when I want to make an "electron.dat" file which includes the atomic
number for each atom name in the system, I have more than one line for some
atom names, e.g. for N, C, and H atoms.
In an ideal case, the atom names should be different in order to the
interpret the gmx density output without any confusion.
However, I think I could/should keep just one line for each atom name
because there is no difference in their atomic number between the lipids.
Based on the code, it seems that when a group is selected from
an index.ndx file, the partial charges for that specific atom (i.e. atom
name N from residue lipid1) is taken into account and added to the atomic
number defined in the "electron.dat". This way, it seems both having one
line and three lines for an atom name (e.g. N) will give the same results,
as gmx density can recognize this based on index group.

I would like to know your opinion on this.
Thanks in advance for your comments

Cheers,
Mohsen


On Tue, Jan 16, 2018 at 10:16 AM, Mohsen Ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

> Thanks, Justin.
>
> I will as you recommended.
> The last approach was described in a book chapter for bilayer simulation.
> I had difficulty to justify that approach.
>
> Cheers,
> Mohsen
>
>
>
> 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
>>> 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
>>
>> --
>> ==================================================
>>
>> 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
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
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>
>
>
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