From: . Juita (juita_at_uon.edu.au)
Date: Fri Jan 31 2014 - 00:55:55 CST

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
[https://mail.google.com/mail/u/1/images/cleardot.gif]

On Thu, Jan 30, 2014 at 4:13 AM, Ali Alizadeh <ali.alizadehmoj_at_gmail.com<mailto: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<mailto: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