[gmx-users] How to obtain MSD trajectory for only one direction from g_msd ??

[Justin Lemkul]

On 11/22/12 5:44 AM, Kiwoong Kim wrote:
> Hi,
>
> It seems that the one directional diffusion constants can be obtained by
> means of g_msd ...blabla...-type z.
>
> However, my question is that I don't want to obtain the diffusion constants.
>
> Actually, the MSD trajectory file for all 3 dimensional data can be
> obtained by conventional g_msd...
> Instead, I want to obtain MSD (time)trajectory file (.xvg file) that
> contain only one directional, say z, data.
>
> I want to analyze it and regress it by curve fitting from the MSD data.
>
> How can I do this ?
>

The only useful output file from g_msd is msd.xvg (the default output).  Does 
this not contain what you want?  The help description seems to suggest it does. 
  If, for some reason, this is not the information you're after, you'll probably 
have to modify the code yourself to produce the desired output, but it seems to 
me that MSD will be written to msd.xvg under the parameters (i.e. direction) you 
specify.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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