[gmx-users] Doubt regarding gmx msd

sanjeet kumar singh ch16d012 ch16d012 at smail.iitm.ac.in
Sat Jun 23 14:51:46 CEST 2018

Dear gmx users,
                    I want to calculate mean square displacement (MSD) for
three chains in my system. And for this i have prepared separate index file
for all the three chains in my system. And i am running the gmx msd command
using these index file. But i am confused as how i can interpret the data
in the output .xvg file which i got after running the gmx msd command.

In the output  file there are msd values for different times separated by
the interval of 5 ps (the time interval i used to store the data in .xtc

I went through some of the post related to gmx msd command. And i am
confused with the option -trestart. If i am giving suppose -trestart as 1
ns for a trajectory file of 240 ns. Then in my output file i should get
data points separated with the time interval of 1 ns rather than 5 ps?

 I am clear that msd results are averaged over all the atoms but how they
are averaged over different restart times for each time in the output file
i.e. i my case 0,5 ps etc. and at last i am getting in my output file data
points separated by an interval of 5 ps instead of 1 ns (trestart time).

Looking forward to you all for clearing my doubt


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