Hi Justin, Here is what I understand. I would like to know if I understood correctly.
Given a selection, which has all the heavy atoms (5 atoms) in the side chain of one specific residue (say Lysine), I want to have only "one value" for the average fluctuation of this selection. Thus, I will use "-res" option in gmx_rmsf command. If I understood correctly, the RMSF for each atom in this selection is calculated first. So, we will have the rmsf(i) values, which i=1 to 5. Next, a mass-weighted average will be taken over all of these atoms. Thus, the final value I get as output is the following: RMSF per selection = (Sum (m(i)*rmsf(i)))/(Sum m(i)) where m(i) is the mass for atom i. Is this correct? If yes, why the RMSF per selection should be a mass-weighted? In other words, whey the usual average is not used, e.g. (Sum (rmsf(i))/5) where 5 is the total number of atoms in this selection. Thanks Mohsen On Thu, May 25, 2017 at 12:54 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/24/17 4:12 PM, Mohsen Ramezanpour wrote: > >> 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? >> >> > The total RMSF of the selection is computed, then a mass-weighted average > over each of the atoms is computed and that subsequent value assigned for > output. See the "average_residues" function in > src/gromacs/gmxana/gmx_rmsf.cpp > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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. > -- *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.