[gmx-users] g_rmsf Analysis.

Justin Lemkul jalemkul at vt.edu
Thu Apr 25 16:22:41 CEST 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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