[DFTB-Plus-User] Bader Charge Analysis

Sharma SRK Chaitanya Yamijala sharmajncasr at gmail.com
Tue Aug 25 14:35:02 CEST 2015


Could you please just tell me the steps what you have done to get charge
difference plots (I just need commands, no need of description) before
using vmd?








********************************************************
*Chaitanya Sharma,*
*Prof. Pati'*s group,
Chemistry and Physics Materials unit,
JNCASR, BANGLORE,
Lab:: (080-2208) 2581, 2809
https://sites.google.com/site/sharmasrkcyamijala/
*********************************************************

On Tue, Aug 25, 2015 at 5:50 PM, Ozan Dernek <ozandernek at gmail.com> wrote:

> I have tried it, and after receiving your mail tried once more, but it
> gives nothing for the negative isovalue since the range starts with a
> positive value.
>
> Regards Ozan
>
> 25 Ağu 2015 tarihinde 14:41 saatinde, Sharma SRK Chaitanya Yamijala <
> sharmajncasr at gmail.com> şunları yazdı:
>
> You need to change one of the Iso-surface value to be negative. If you are
> using command line, see the below example:
>
> mol selection all
> mol material Opaque
> mol addrep 0
> mol modstyle 1 0 Isosurface 0.000400 0 0 1 1 1         # positive value
> for Isosurface
> mol modmaterial 1 0 AOChalky
> mol modcolor 1 0 ColorID 31
> color change rgb 31 0.840000 0.420000 0.110000
>
> mol selection all
> mol material AOChalky
> mol addrep 0
> mol modstyle 2 0 Isosurface -0.000400 0 0 1 1 1      # negative value for
> Isosurface
> mol modcolor 2 0 ColorID 23
>
> HTH,
> Sharma.
>
>
>
>
>
>
>
>
> ********************************************************
> *Chaitanya Sharma,*
> *Prof. Pati'*s group,
> Chemistry and Physics Materials unit,
> JNCASR, BANGLORE,
> Lab:: (080-2208) 2581, 2809
> https://sites.google.com/site/sharmasrkcyamijala/
> *********************************************************
>
> On Tue, Aug 25, 2015 at 4:43 PM, Ozan Dernek <ozandernek at gmail.com> wrote:
>
>> Hi,
>>
>> First of all, I would like to plot the difference in charge densities,
>> but I can only see positive values . As you explained in the website, I
>> first create a CPK rep, then make two isosurfaces, which only have positive
>> isovalues. Is it because the code I am using to make the bader charge
>> analysis, or should I do something via VMD ?
>>
>> Thank you for your attention,
>> Regards,
>> Ozan Dernek
>> 22 Ağu 2015 tarihinde 07:54 saatinde, Sharma SRK Chaitanya Yamijala <
>> sharmajncasr at gmail.com> şunları yazdı:
>>
>>
>> On Sat, Aug 22, 2015 at 4:47 AM, Ozan Dernek <ozandernek at gmail.com>
>> wrote:
>>
>>> file from the structures that I am working on , the minimum isovalue is
>>> always bigger than zero.
>>
>>
>> Dear Ozan,
>>
>> As you understood, if you want to plot charge density then it will be
>> (should be) with all positive values. If you are plotting MOs or
>> spin-densities or "difference in charge densities" etc. then you will be
>> able to see a negative value in cube file. So, if you just would like to
>> see the charge density on an atom, I guess, you should get all positive
>> values.
>>
>> Also, though I am not sure, something like taking the difference between
>> "full system's charge-density" and the "sum of charge-densities of all
>> atoms (except for the one where you would like to see the charge)" may give
>> you some hints about charge transfer from/to the atom of your interest (if
>> this is what you are looking for!).
>>
>> HTH,
>> Sharma.
>>
>> P.S.: If you are dealing with systems with high charge fluctuations and
>> if you haven't done the calculations with DFTB3, then my suggestion would
>> be to stick to DFTB3 than SCC-DFTB. I guess you might have already started
>> with DFTB3.
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ********************************************************
>> *Chaitanya Sharma,*
>> *Prof. Pati'*s group,
>> Chemistry and Physics Materials unit,
>> JNCASR, BANGLORE,
>> Lab:: (080-2208) 2581, 2809
>> https://sites.google.com/site/sharmasrkcyamijala/
>> *********************************************************
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