[gmx-users] g_rmsf Analysis.

[Justin Lemkul]

On 4/25/13 10:12 AM, Vivek Modi wrote:
> Hello,
>
> I am using g_rmsf for analysis of a protein simulation. I want to calculate
> the fluctuations with respect to a reference structure (using -od option).
> But I am encountering a problem. Please correct me if I am wrong at some
> place. The following two methods are giving me different results. I have
> defined the residues forming helices as a separate group in the index file
> (to exclude loops).
>
> 1. g_rmsf  -f abc.xtc -s abc.tpr -od rmsdev.xvg -n index
> --> I choose  Protein_CA from the index file (full protein).
>
> 2. g_rmsf  -f abc.xtc -s abc.tpr -od rmsdev.xvg -n index
> --> I choose helix_residues_CA from the index file (excluding loops).
>
>
> For the same helical regions of the protein I am getting different results
> from these two methods. The first one shows high fluctuations as compared
> to the second. My guess is that it can be due to different fitting by the
> choice of different atoms. But I suspect that the difference between the
> two is quite big than to be caused by different fitting.
>

I would counter that differences in fitting can quite easily explain the 
difference you are seeing.  Without the actual numbers, it's hard to say exactly.

> I also repeated the same analysis by dividing the trajectory into two parts
> and comparing the fluctuations with each other and the for the complete
> trajectory.
> The output in this case from the first method was consistent. Same regions
> were showing similar fluctuations. But for the second method the chunked
> parts of the trajectory displayed very small movement in certain regions
> where the complete trajectory analysis exhibited high fluctuations. How can
> this be inconsistent for the same fitting.
>

Simply splitting the trajectory in half is not necessarily informative, 
especially if the structure is sampling different states, is not equilibrated in 
the beginning, etc.

-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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