[gmx-users] a simple doubt about g_rms

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 4 21:39:34 CET 2010

Miguel Quiliano Meza wrote:
> Hi everyone.
> Nowadays I am learning how to analyze my results after MD. I have been 
> reading the tutorial "GROMACS Tutorial for Drug – Enzyme Complex" and 
> all is fine but I have a big doubt about g_rms. I know that g_rms 
> compares two structures by computing the root mean square deviation 
> (RMSD). In the tutorial one part said:
> "Use g_rms to obtain an RMSD plot of the protein backbone and the drug 
> (IN4) throughout the simulation. Do the Backbone first g_rms –s md.tpr 
> –f md.trr (or xtc) –o bkbone_rmsd.xvg You will be prompted to select a 
> Group. Enter 4 (for backbone).
> Compare to 1 Group in the reference. Enter 1 then Enter 4 for backbone 
> again."
> The last part for me is confused, I understand that I am going to 
> compare backbone with protein so first (4) and then (1), but "Enter 1 
> then Enter 4 for backbone again", why???? and what should I do if I want 
> to calculate the RMSD of the drug? (4) and then LIG?? or (LIG) and (LIG)?

The two groups serve two purposes - the first entry (per the prompt) is the 
group for which the least squares fit is performed.  The second group (the 
calculation group) then has the RMSD calculated from the fitted orientations. 
Lots of textbooks and web resources explain the calculation in greater detail; I 
suggest you have a look to see what Google will offer you, as well :)


> I know that these are trivial questions but I would be grateful I 
> someone can help me or give advices.
> Thanks in advance.
> Miguel.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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