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
--
========================================
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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