[gmx-users] how to get the block averaged MSD curve ?

Kiwoong Kim ilmarejoe at gmail.com
Thu Feb 9 12:25:46 CET 2012


I have a simulation result from 0 to 50ns after equilibration run.
I want to divide this data set equally into 10blocks (10ns each) and get
block averaged MSD curve (average of 10 blocks).

It seems that I mange to get block MSD data by using  g_msd -beginfit 0
-endfit 10, g_msd -beginfit 10 -endfit 20,....
Then the output files are msd1.xvg, msd2.xvg,......,msd10.xvg (10 xvg files)

My question is that how can I get averaged MSD from this outputs??
It seems that g_analyze is appropriate to do this.

g_analyze -n 10 -av ??

Could anybody tell me how to get averaged MSD using g_analyze (each block
data has different x values but same length) ?

Another question is that
what is the difference bwn g_msd and g_analyze -msd ??
Is there any reference of posting to obtain this information ?
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