Dear Gromacs users, I have a question on RMSF calculation:
I am not sure how -res works in RMSF and I could not find any useful explanation for it. It will give the average fluctuations per residue, fine. but how exactly? 1) it calculates the RMSF for each atom in that residue first. Then, it averages over all of these atoms and reports it as the average for the residue. 2) it takes the center of mass or specific atom of the residue and calculates the RMSF for that. Or something else? I am interested in the average fluctuation for sidechain of one residue (excluding H atoms from this calculation). I want to have only one value as the average fluctuation for this group. I choose the residue-sidechain-H group (which I made in an index file) when prompted in the following command: gmx rmsf -f md.xtc -fit -s md.tpr -n index.ndx -o residues-sidechain-H.xvg -res an alternative would be to use the following command and make an average over all atoms manually: gmx rmsf -f md.xtc -fit -s md.tpr -n index.ndx -o residues-sidechain-H.xvg The results are NOT the same as expected. I think I should use the second command and make the average manually. What do you think? Cheers Mohsen -- *Rewards work better than punishment ...* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.