[gmx-users] helical parameters for DNA

[Justin A. Lemkul]

shahab shariati wrote:
> Hi gromacs users
>  
> I want to simulate pr-dna by gromacs.I read a article (Biophysical 
> Journal 87(6) 3799–3813) inwhich helical parameters for DNA (rise, 
> slide, twist, roll, tilt, shift) calculated by md simulation, but I did 
> not understand two things:
>  
> How and what command these parameters were calculated?
>  

There's nothing in Gromacs that will do all that by default.

> I read gromacs manual. in that there is only  g helix  and  g 
> helixorient  for Protein specific analysis.
>  
> can any body help me how to do this ?

You'll probably have to code it yourself.  These are all simple geometric 
parameters, so it shouldn't be that difficult.

-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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