you are right, I shall take more respect of the results.
in the paper mentioned above, they didn't mention the solvation box, they should just do it only with base pairs.
but what shall I do with my simulation of G-C pair in water box, it seems all right that the bases fly apart or they form stacking but not pair during equilibrium step. but I can't perform vibrational analysis to check the H-bond effect on the sturcture.
but is it still meaningful go on the simulation and check the sturctural fluctuation?
and by the way, is there any already published paper about base pair simulation ? I didn't find about G-C pair yet.
thank you for your time !
Last edited by ckc1117; 08/04/08 12:58 PM.