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

[Hwankyu Lee]

Dear, gmx-users,

These days, I asked some questions on using g_density for electron 
densities, and got some answers from friendly gmx-users. Now, I would 
like to put an answer from prof. Peter Tieleman below.

----------------------------
Uhm, you shouldn't. That is wrong in the paper, and I missed it before 
it went
to press. Atoms have a fixed number of electrons, no partial charges 
involved.
g_density just needs a file with the atom names and the number of 
electrons in
each of those atoms.

Peter
-----------------------------

best,
Hwankyu.


On Mar 2, 2004, at 4:17 PM, Hwankyu Lee wrote:

> 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?
> Thanks for your help in advance.
>
> 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
>>>> answer for your 2nd question.
>>>>
>>>>   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?
>>>>>
>>>>> Thanks for your help in advance.
>>>>>
>>>>> best,
>>>>> Hwankyu.
>>>>>
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