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

[Francesco Oteri]

Il 15/04/2011 18:45, Alok Jain ha scritto:
> 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 ??
>
> Thanks in advance.
>
> Alok
The reason is that in the two cases you used two different groups to fit 
the protein.
Different fit generates different result. If you try to calculate RMSF, 
fitting on the subunit B, you will find a third result. I guess the 
subunit B should fluctuate less than case 2)