# [gmx-users] A question on using g_density for electron densities.

Hwankyu Lee leehk at umich.edu
Tue Mar 2 22:19:01 CET 2004

```I appreciate you for your answer again.  I think it is a good idea, but
I would like to make sure if it  is right with listening to more
people's opinions.
Therefore, I would like to know the exact meaning of this sentence in
the GROMACS manual:
"the number of electrons for each atom is modified by its atomic
partial charge."
How could we modify # of electrons by using partial charge?

best,
Hwankyu.

On Mar 1, 2004, at 4:27 PM, Zhen Qin wrote:

> You are welcome. The value is calculated by myself, # of electrons plus
> the value of partial charge shown in my lipid.itp file. In the manual
> of
> GROMACS, it is said " the number of electrons for each atom is
> modified by
> its atomic partial charge."  So, I added it up. I hope it is correct.
> :-)
> For united atoms or dummy atoms, make sure to take the partial charge
> into
> consideration. :-)
>
> Good luck.
>
> -Zhen
>
> Have a good day !  ^&^
>
> On Mon, 1 Mar 2004, Hwankyu Lee wrote:
>
>> Thanks for your help. Now I can get electron density profiles, but I'm
>> wondering how you get accurate values like you said below.  Also, I
>> would like to make sure if we don't need to consider H atoms in C1,
>> C2,
>> and so forth because of united atoms.  Do you have any ideas about
>> dummy atoms in proteins like MNZ1, MN1?
>>
>> best,
>> Hwankyu.
>>
>>
>> On Mar 1, 2004, at 1:16 PM, Zhen Qin wrote:
>>
>>> Hi. I used g_density a couple of times. I guess your file format is
>>> not
>>> very accurate. This is my file
>>> 61
>>>  OW = 7.18
>>> HW1 = 1.41
>>> HW2 = 1.41
>>>  N1 = 6.5
>>>  C2 = 6.4
>>>  C3 = 6.4
>>>  C4 = 6.4
>>>  C5 = 6.3
>>>  C6 = 6.4
>>>  O7 = 7.2
>>>  P8 = 16.7
>>>  O9 = 7.2
>>> O10 = 7.2
>>> O11 = 7.3
>>> C12 = 6.4
>>> C13 = 6.3
>>> O14 = 7.3
>>> C15 = 6.7
>>> .....
>>> C57 = 6
>>> C58 = 6
>>>  It works. You can have a look. Sorry it is a lipid, I donot know the
>>>
>>>   Good luck.
>>>
>>> -Zhen
>>>
>>> Have a good day !  ^&^
>>>
>>> On Mon, 1 Mar 2004, Hwankyu Lee wrote:
>>>
>>>> Dear, gmx-users,
>>>>
>>>> I'm trying to analyze electron density of my systems, but I couldn't
>>>> find enough answers in gromacs homepage. Therefore, I have some
>>>> questions.
>>>>
>>>> 1) When I used -ed option, I got an error like "Fatal error: Invalid
>>>> line in datafile at line 1".
>>>> I made electrons.dat file like below. (let's say that the number of
>>>> atoms are 85)
>>>> --------
>>>> 85
>>>> C1=6
>>>> C2=6
>>>> OW=8
>>>> HW1=1
>>>> HW2=1
>>>> Cl=17
>>>> Na=11
>>>> and so forth......
>>>> --------------
>>>> Is there something wrong with this?  If so, could you show me short
>>>> examples like a simple water box (3atomnames, OW, HW1, and HW2) ??
>>>>
>>>> 2) I'm wondering if I need to write down all the atomnames and # of
>>>> electrons. I'm using 25 residue protein, therefore do I need to put
>>>> all
>>>> the atomnames of those  residues into electrons.dat by hand?
>>>>
>>>>
>>>> best,
>>>> Hwankyu.
>>>>
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