Thanks a lot for your answer. 2013/5/10 Justin Lemkul <[email protected]>
> > > On 5/10/13 4:24 AM, Nawel Mele wrote: > >> Hi, >> >> I am trying to understand what is the difference between g_rms and >> g_rmsdist commands. >> I have looked at the manual and all I can find is that: >> >> *g_rms*: The root mean square deviation (RM SD) of certain atoms in a >> >> molecule with respect to a reference >> structure can be calculated with the program g_rms by least-square fitting >> the structure to the reference >> structure (t2 = 0) and subsequently calculating the RMSD >> * >> g_rmsdist*: Alternatively the RMSD can be computed using a fit-free method >> >> with the program g_rmsdist >> >> >> >> What fit is this referring to ? >> >> > RMSD is normally calculated after a least-squares fit to eliminate the > influence of global rotations and translations that would otherwise result > in spuriously high RMSD values. In the case of g_rmsdist, no fitting is > done, and has different applications (explained in the help description). > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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 [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- *Mlle* Mele Nawel Master 2 In Silico Drug Design University of Paris Diderot/Strasbourg -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
