On 9/21/16 5:50 AM, Seera Suryanarayana wrote:
Dear gromacs users, Previously I posed a problem how to calculate the RMSD of our interested region of protein, even though I did simulation for full length protein. I got solution from one of our user. Based his suggestion I created index file and have executed the following command. gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns -n index.ndx My index.ndx file has the c alpha numbers which I have to calculate the RMSD. Here I am not mentioning any superimposition. How does the gmx rms command work? can I do superimposition of my interested residues? and also what is -fit argument? I request you to answer my question.
The first group gmx rms prompts for is the fitting group, applying whatever type of fitting is requested in -fit. The default is rotational and translational fitting, which is usually what one wants to avoid spurious global contributions to the RMSD.
-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.
