VMD-L Mailing List

From: Ali Alizadeh (ali.alizadehmoj_at_gmail.com)
Date: Thu Jan 30 2014 - 06:57:55 CST

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