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

[Tsjerk Wassenaar]

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.
>
>>
>> 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 ?
>>
>>
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands