From: Ali Alizadeh (ali.alizadehmoj_at_gmail.com)
Date: Fri Jan 31 2014 - 12:45:41 CST

Dear Juita,

Sorry to late response.

I think you are right(unit of simulation time). It's so easy for checking
it. I always did unit conversion for checking the self diffusion values
with literature's.

If you have access to a strong supercomputer, I strongly recommend you
performing longer simulation.

On Thu, Jan 30, 2014 at 10:55 PM, . Juita <juita_at_uon.edu.au> wrote:

> Dear Ali,
>
>
> Thank you very much for the information. This plugin is really useful.
>
> However, I still get the self-diffusion coefficient value 100 times less
> than the literature value. I suspect that it is related to the unit of
> simulation time. In the input file, I specified the time step as follows:
>
> TimeStep [Femtosecond] = 1
> MDRestartFrequency = 100
>
> So the time between frames is 100 fs. I would like to double check if it
> is right. May I know if anyone has similar issue as me? Any suggestions
> would be appreciated.
>
>
> Many thanks and best regards,
>
> Juita
> ------------------------------
> *From:* owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of
> Ali Alizadeh <ali.alizadehmoj_at_gmail.com>
> *Sent:* 30 January 2014 23:57
> *To:* Vmd l
> *Subject:* Re: vmd-l: self-diffusion coefficient from RMSD
>
> Dear Juita,
>
> I think you can calculate this property by using this plugin for VMD:
>
> http://multiscalelab.org/utilities/DiffusionCoefficientTool
>
>
> On Thu, Jan 30, 2014 at 4:13 AM, Ali Alizadeh <ali.alizadehmoj_at_gmail.com>wrote:
>
>> Dear Juita,
>>
>> I think you can calculate this property by using this plugin for VMD:
>>
>> http://multiscalelab.org/utilities/DiffusionCoefficientTool
>>
>>
>>
>> On Thu, Jan 30, 2014 at 1:21 AM, . Juita <juita_at_uon.edu.au> wrote:
>>
>>> Dear VMD users,
>>>
>>> I am doing calculation of self-diffusion coefficient from the
>>> trajectories data obtained from DFTB+ simulation. I am wondering whether I
>>> do the correct calculation. I utilise VMD to calculate and plot the RMSD,
>>> then squared it to get the plot of MSD (mean square displacement). The
>>> self-diffusion coefficient is estimated from the slope of MSD vs time plot
>>> using Einstein relation. However, I get the value 100 times less compared
>>> to the literature value. I would appreciate any assistance for this problem.
>>>
>>> Thank you so much for your assistance.
>>> Best regards,
>>> Juita
>>>
>>
>>
>>
>> --
>> Sincerely
>>
>> Ali Alizadeh
>>
>
>
>
> --
> Sincerely
>
> Ali Alizadeh
>

-- 
Sincerely
Ali Alizadeh