[gmx-users] Re: helical parameters for DNA

Attilio Vargiu vargiu at sissa.it
Tue Jun 8 14:14:17 CEST 2010

you can use for example Curves (Nucleic Acids Research, 2009, Vol. 37, No.
17 5917-5929) or 3DNA
(http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html) to calculate them
from any trajectory, I did but never used gromacs for this, I don't know
if it is possible.

Hope this helps,

2010/6/8 shahab shariati <shahab.shariati at gmail.com>

    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?

    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 ?

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                 Attilio Vittorio Vargiu, PhD
  SLACS & Department of Physics, University of Cagliari
 Cittadella Universitaria S.P. Monserrato-Sestu Km 0.700
              09042 Monserrato (CA), Italy

            e-mail1: vargiu at dsf.unica.it
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