From: Vermaas, Joshua (
Date: Sun Sep 30 2018 - 18:06:15 CDT

Hi Kinkini,

I can't speak to why the plugin is misbehaving, but the MSD = t * D/(2d), with D being the diffusion constant you want to calculate, d being the number of dimensions considered for diffusion, and t being time. Over short timescales, your diffusion can often be overestimated, but fitting the slope over longer timescales usually works. My advice is to first plot your MSD vs time in something like Excel and do the linear fit there so you have something to compare with, since the slope is related to your D value.

Of the scripts you linked to, the matlab code is more readable to a newcomer, since it uses POLYFIT to compute the linear regression. The fortran version does the same thing, its just not as easy to read.


On 2018-09-29 11:31:52-06:00 wrote:

Dear All,
I have modeled a water droplet of 3173 atoms which includes 10 Hydronium ions ,formate ions as counter ions and one acetaminophen (+1) molecule.The droplet radius is 2 nm and simulation was run for 400ns.
I am looking for the diffusion coefficient of acetaminophen.For that I used Diffusion coefficient plugin in VMD
 ( Toni Giorgino, Computing diffusion coefficients in macromolecular simulations: the Diffusion Coefficient Tool for VMD, Submitted (2015)).
I have trouble with this plugin. Every time I used absolute frames numbers of my trajectory (1500 frames with 1fs time step,because I loaded only first few frames of the 400ns trajectory ) it gives an error message "domain error :argument is not in a valid range" but when I used the default values it calculates the diffusion coefficient ONLY for formate ion ,hydronium ions not for the acetaminophen.For the acetaminophen it gives zero diffusion coefficient when only default values are given for the lag times and analysis interval.
Before I used the plugin, I have calculated the how far acetaminophen diffused throughout the simulation using VMD distance.tcl script .The data clearly shows the acetaminophen diffused well and also from the visualization of the trajectory ,it can be observed the molecule is diffusing well.So anyone who is familiar with the diffusion coefficient plugin in VMD I would be appreciated for your thoughts about this error.
Also,I have calculated MSD values for the first 1500 frames using a in house built script.But, I don't know how to build a script or any method to get diffusion coefficient using those MSD data.(I am an amateur computational chemist ) But, theoretically there is linear relation between diffusion coefficient and MSD .I found this following article which has mentioned about a script to get the diffusion coefficient but Im not very much clear about the code.So,I would be really great full if anyone can share a script or method to calculate Diffusion coefficient using MSD data or help me to understand the method/script mentioned in below article .>
So,any insight would be greatly appreciated.
Thank you in advance!
Kinkini Jayasundara
Phd student
Chemistry Department
West Virginia University