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
--
========================================
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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