[gmx-users] helical parameters for DNA

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 8 13:42:42 CEST 2010

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 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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