[gmx-users] g_msd

Mark Abraham mark.abraham at anu.edu.au
Tue Jul 13 02:22:02 CEST 2010

On 13/07/10 07:22, Ricardo Cuya Guizado wrote:
> 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?

It's hard to offer help, because your description is incomplete. How 
large is the system? Should the protein be stable? What was the 
equilibration regime? What was the reference structure for fitting? What 
were your g_msd command lines? What were the MSDs reported?

You should upload your plots to some free site that hosts images/files, 
and provide a link, rather than make a general description of them.

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