[gmx-users] Query of RMSD results

Justin Lemkul jalemkul at vt.edu
Tue Nov 4 22:28:17 CET 2014

On 11/4/14 9:24 AM, Sainitin Donakonda wrote:
> Hi Justin,
> Thanks for reply,  i plotted RMSF for all complexes and protein only please
> check both RMSD and RMSF plot in following link.
> http://sainitindonakonda.weebly.com/
> Now in RMSF plot ligand 1 fluctuates slightly higher than protein-only. Im
> confused :( i am not getting what to interpret for protein-ligand 1 complex
> as it looks different in both RMSD and RMSF. Can you please give an
> explanation on this point.  And also give more information about what is
> the difference between RMSD and RMSF.

OK, so this particular analysis, when taking a macro view, doesn't tell you 
much.  Are there differences in atoms nearby to the ligand?  What about hydrogen 
bonding? Contacts? Energetic analysis?  There is a lot of stuff you can do.  No 
one on this list is going to be able to do your work for you, though.  Watch the 
trajectories, see if there is something that you can find by doing the easiest 
thing - looking.

As for RMSD and RMSF, Google, Wikipedia, and the Gromacs manual all know a ton 
about these.  Doing a bit of homework before diving into the actual research 
will probably alleviate much of your confusion.



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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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