**From:** Kinkini Jayasundara (*kuj0001_at_mix.wvu.edu*)

**Date:** Fri Sep 28 2018 - 20:48:39 CDT

**Next message:**Wintrode, Patrick: "RE: Mismatch in atom number between psf and dcd files"**Previous message:**Vermaas, Joshua: "RE: Mismatch in atom number between psf and dcd files"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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 .

http://utkstair.org/clausius/docs/che548/pdf/selfD.pdf

So,any insight would be greatly appreciated.

Thank you in advance!

Kinkini Jayasundara

Phd student

Chemistry Department

West Virginia University

E-mail :kuj0001_at_mix.wvu.edu

**Next message:**Wintrode, Patrick: "RE: Mismatch in atom number between psf and dcd files"**Previous message:**Vermaas, Joshua: "RE: Mismatch in atom number between psf and dcd files"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Tue Sep 17 2019 - 23:20:13 CDT
*