[gmx-users] regarding rmsd and gyrate

[Justin A. Lemkul]

priya thiyagarajan wrote:
> hello sir ,
> 
> i got few basic doubts in dynamics..
> 
> while performing analysis, we are calculating rmsd and gyrate  for 
> single molecule..
> 
> but in case of more molecules i.e by adding 20 molecules randomly using 
> genbox , when we perform analysis, rmsd value we are obtaining is the 
> average change in structure deviation from initial structure.
> 
> what about gyrate??
> 
> i am getting one plot... how to interpret the result for 20 
> moecules..since 20 molecules arranged randomly, how it calculates the 
> gyrate value..
> 
> please help me with your answer..
> 

I think g_polystat is more appropriate in this case.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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