VMD-L Mailing List

From: Nakshatra Upadhyay (1225nakshatraupadhyay1975_at_gmail.com)
Date: Wed Aug 09 2023 - 15:04:29 CDT

Hi Josh,
Thank you for getting back to me so quickly. I used Gromacs trajectory to
calculate the diffusion coefficient. And I considered that those are
unwrapped. But I used the vmd unwrapped option and now got a reasonable but
relatively high diffusion coefficient value, i.e., ~5.09 m^2/s.
Sincerely yours,
Nakshatra

On Wed, Aug 9, 2023 at 8:49 PM Josh <vermaasj_at_msu.edu> wrote:

> Hi Nakshatra,
>
> Did you use a wrapped trajectory? Knowing very little about the
> diffusion coefficient tool, which isn't part of a standard VMD
> installation, that is where I'd guess things went wrong. If you have a
> simulation that is wrapped, the mean squared displacement found in the
> trajectory is bounded by how big your box is, which is why you often
> will unwrap your trajectory prior to calculating a diffusion coefficient.
>
> -Josh
>
> On 8/9/23 12:25 PM, Nakshatra Upadhyay wrote:
> > Dear all,
> > I have been trying to calculate the diffusion coefficient of water
> > using VMD Diffusion Coefficient Tool. However, I got an extremely low
> > diffusion coefficient value for water (Experimental value ~2.3 m^2/s),
> > 0.0002266 angstrom^2/ns (2.66 m^2/s) was the fit value for diffusion
> > coefficient. I used a 100ns trajectory having 5000 frames (data saved
> > in every 10000 steps and time step was 2.0 fs) to calculate the
> > diffusion coefficient. I used 500 to 2501 frames as lag time and
> > calculated the diffusion coefficient with a 100-frame interval
> > (Although I got almost the same values with different lag times). The
> > VMD Diffusion Coefficient Tool calculated MSD value was almost
> > constant (~720 angstrom^2) for the selected lag time. Could you please
> > suggest me how to calculate the diffusion coefficient using VMD?
> > Sincerely yours,
> > Nakshatra
>
> --
> Josh Vermaas
>
> vermaasj_at_msu.edu
> Assistant Professor, Plant Research Laboratory and Biochemistry and
> Molecular Biology
> Michigan State University
> vermaaslab.github.io
>
>