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

[Kiwoong Kim]

I gratefully  appreciate to your reply Justin.

You are right, it seems that g_msd provides the MSD.xvg file what I want
(in one direction).
I was confused before.

Thanks again.


2012/11/23 Justin Lemkul <jalemkul at vt.edu>

>
>
> 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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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