[gmx-users] pi-stacking energy between carbon nanotube and nucleic acids

[soumadwip ghosh]

Dear users,
                  I was wondering which is the more realistic way to find
out the stacking energy between a DNA base and a single wall carbon
nanotube. I am interested in evaluating pi-stacking interactions between
individual residues and a Chiral carbon nanotube. In some of the papers
they calculate the interaction between DNA strand and carbon nanotube using
various free energy estimations (MM-PBSA, TBI or free energy perturbation
techniques) but isn't it the short range LJ forces from
the appropriate energy groups in the .edr file that should be more
realistic?

Also, when I am calculating RMSD with respect to the initial structure it
was my expectation that the residue which gets stacked more strongly would
have the highest magnitude of RMSD as compared to the initial structure but
I am getting the order reversed. Is there something wrong in my assumptions?

Any kind of help will be of great help. Thanks for your time in advance.

Regards,
Soumadwip Ghosh
Research Fellow,
Indian Institute of Technology, Bombay,
India.