[gmx-users] Calculating diffusion coefficient in three dimension

[Venkat Reddy]

Thank you sir for the prompt reply.
*g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu ns*
Here I am giving -lateral z (like for membrane simulations). Is it fine for
spherical systems also?


On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:

> MSD is 3D by default.
>
>
> Dr. Vitaly V. Chaban
>
>
> On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy <venkat4bt at gmail.com> wrote:
> > Dear all,
> > I am simulating a spherical lipid vesicle. I want to calculate the
> > diffusion coefficient for each lipid component in 3D. How to calculate it
> > using g_msd (or any other tool like g_velacc)?
> >
> > Thank you for your concern
> >
> > --
> > With Best Wishes
> > Venkat Reddy Chirasani
> > --
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036