[gmx-users] deformation of DNA duplex

[soumadwip ghosh]

Hi all,
        I have a couple of quick questions. I am simulating DNA duplex with
some fullerene derivatives. The fullerenes are expected to accommodate
themselves in the major groove of the DNA and I am getting similar results.
However, the parallel DNA chains are getting deformed which is also
expected. My question is apart from H-bonds is there any way by which one
can show that the DNA is getting significantly deformed as compared to its
native structure? In the given link below, people have used roll, twist,
curl and slides to probe the DNA deformation. Is there any way I can
calculate those parameters from GROMACS?
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439907/pdf/gks517.pdf

How can I show the time evolution of fraction of native contacts for my DNA
chain?

Sorry if I am asking for much. Thanks for your time in advance.

Regards,
Soumadwip Ghosh
Research Fellow,
IITB
India