[gmx-users] RMSF: Different results for same residue

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 15 18:52:22 CEST 2011

Alok Jain wrote:
> Hi,
> I am simulating a tetrameric protein in membrane. The simulation is
> for 30ns. I wish to calculate RMSF for just one monomer (A).
> I thought of doing this in two ways,
> 1. I input the residue numbers for the monomer A by creating an
> index.ndx file to calculate RMSF only for the selected monomer CA
> atoms.
> g_rmsf -f  *.xtc -s *.tpr -od rmsdev.xvg -n index.ndx
> 2. I calculate RMSF for the complete protein CA atoms
> g_rmsf -f *.xtc -s *.tpr -od rmsdev.xvg
> I find the output from these to commands for the same monomer A
> residues are different. The second command calculates a very high RMSF
> for the same residues.
> Why is it so ?? Or am I making a mistake at some place ??

The selected index group has a least-squares fit performed on it.  If the 
fitting group is different, the output RMSF will be different.  In case (1) 
you're doing the fitting and establishing a reference for RMSF from just one 
monomer and then doing the calculation on that group.  In case (2) you're using 
the whole protein for the calculation.


> Thanks in advance.
> Alok


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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