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

[David van der Spoel]

On 2012-02-10 10:35, Tsjerk Wassenaar wrote:
> Well, I don't think excel will be a convenient tool for this. Why not
> try awk for a change?
>
> paste msd*.xvg | awk '/^[^@#&;]/{S=0;N=0; for (i=2;i<21; i+=2)
> {S+=$i;N++}; print S/N}'
>
> Otherwise a few lines of python would also do the trick.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Feb 9, 2012 at 1:56 PM, lina<lina.lastname at gmail.com>  wrote:
>> 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.
>>

g_msd -h


>>>
>>> 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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>
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se