[gmx-users] g_msd

Ricardo Cuya Guizado rcuyag at hotmail.com
Mon Jul 12 23:22:15 CEST 2010

Dear gromacs users 
I make a MD of 20 ns of a solute in water
With the g_msd program the msd vs the time was obtained 
In the plot, I observed a linear behaviour of the MSD from 0 to 15 ns and a plateau with no linear tendence at the last 5 ns arpoximately.
In order to know if the observed plateau was due to the data or is due to the way as the algorithm process the data, I divided the MD in two trajectories and obtained the msd for each one.
>From 0-10ns, the plot observed shows a linear tendence en the begining and a plateau with no linear tendence from 9 to 10 ns.From 10-20 ns the plot observed was linear from 10 to 18 ns and not linear at the last, the same plateau was observed.
Comparing the plots there are not equivalent,.
Why g_msd produces a non linear plot at the last of the calculation and the plateau is ever produces.
Somebody will explain the way as the g_msd algorithm work? and why the plot are no equivalent or why there must be equivalent?

Ricardo Cuya

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