From: Kinkini Jayasundara (
Date: Sat Sep 29 2018 - 11:30:47 CDT

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