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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
