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

Alok Jain alokjain16 at gmail.com
Fri Apr 15 18:45:13 CEST 2011


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
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.


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