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

lina lina.lastname at gmail.com
Thu Feb 9 13:56:18 CET 2012

On Thu, Feb 9, 2012 at 7:25 PM, Kiwoong Kim <ilmarejoe at gmail.com> wrote:
> Hi,
> 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).

I would try some external software. excel.

> 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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