I am trying to calculate the mean squared displacement and had written a code in fortran. I wrote this code using a reference book by Daan Frenkel and Berend Smit on Molecular Dynamics Simulation. I am having a hard time in getting the exact plot as proposed for a particular system. Can anybody have a look at it and suggest me where I am doing wrong in calculating the Mean Squared displacement as function of time.
Also, I would like to mention a little detail of the code. I used Origin shift method here in code where "i1" is for origin shift and calculating particles displacement over (total_time - 1) for all the particles present in a simulation cell. First, I am averaging over the number of data points (tau) accumulated (due to the shift of origin) for each atom for a particular origin (i1) in loop and finally after accumulating it over total number of particles (ntotal) and averaging it(ensemble_avg).
Dear Anupama Sharma
In statistical mechanics, the mean squared displacement (MSD, also mean square displacement, average squared displacement, or mean square fluctuation) is a measure of the deviation of the position of a particle with respect to a reference position over time.
Kind Regards
Qamar Ul Islam
MSD is defined as MSD=average(r(t)-r(0))^2 where r(t) is the position of the particle at time t and r(0) is the initial position, so in a sense it is the distance traveled by the particle over time interval
Check this video too.
https://www.google.com/url?sa=t&source=web&rct=j&url=https://m.youtube.com/watch%3Fv%3DyZ7zHg7goBc&ved=2ahUKEwj6g_HOterxAhWKXsAKHZBwAYYQFjAOegQIQRAF&usg=AOvVaw2RZgJGRU4_1HYefgr31OSM
I would like to share an article that helped me with the code for mean squared displacement calculation. Hope this will help others who are facing issue with the concept.
Article A New Perspective on the Order-n Algorithm for Computing Cor...
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