On 11/29/19 5:53 AM, Mala L Radhakrishnan wrote:
Hi, I am confused a bit by this answer -- isn't the file specified by -s used for defining the rmsf (this is what is called the "reference" structure in the documentation, and I have found that my results do vary using a different "-s" file)...? Or is that just used for fitting and then the average of the resulting fitted structures is used for the rmsf? Specifically, what is the "-s" uased for in this case?
It is used for fitting. RMSF is simply the standard deviation of position, so an average structure is computed from the selected frames and the RMSF is computed from it.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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.
