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)
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