[gmx-users] Electron density using g_density

[Mohsen Ramezanpour]

Hi All,

I did a short test on this. Following is the results.

I made two electron.dat files,

one like:
1
N = 7

and the second one like:
2
N = 7
N = 7

I also made an index.ndx with these groups:
r lipid1 & a N
r lipid2 & a N

Next, I calculated the electron density for these two groups using two
electron.dat files, separately.

The results are exactly the same.
Cheers


On Wed, Jan 17, 2018 at 9:56 AM, Mohsen Ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

> 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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>>
>>
>>
>> --
>> *Rewards work better than punishment ...*
>>
>
>
>
> --
> *Rewards work better than punishment ...*
>



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