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
========================================
--
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
