[gmx-users] g_rmsf

[Tsjerk Wassenaar]

Hi Efrat,

2011/5/3 Efrat Noy <exlrode at mail.biu.ac.il>:
> Hi,
>
> I have 2 questions regarding root mean square fluctuation calculations:
>
> 1. what exactly is the difference between the values in the rmsf.xvg file
> and the values in the rmsdev.xvg file (obtained with the -od option)? Are
> the rmsf.xvg values are standard deviations of atom positions along the
> trajectory with respect to an average structure of the trajectory? And
> rmsdev.xvg values are the same but in respect to a reference structure
> defined by the tpr file?

The help is pretty clear on the first part: -od gives the RMSD w.r.t.
the reference. You're right on the nature of the RMSF.

>
> 2. Is it possible to fit the trajectory structures, prior to rmsf
> calculations, on only part of the protein?

Yes. You can preprocess the trajectory with trjconv and use the -nofit
option to g_rmsf.

Cheers,

Tsjerk

> Thanks, Efrat
>
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-- 
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