ideal values for the stacking parameters

[Miguel]

Hi,

we have performed a MD simulation of a DNA duplex and have accumulated a series of snapshots. We'd like to understand how the structure of the duplex is changing during the MD. For this, we want to compare the structure for the snapshots to the structure of an ideal duplex, understanding for an ideal duplex one with a uniform structure.

Then,  assuming there are ideal values for the parameters shift, slide, rise, tilt, roll and twist, we want to see how these parameters change during the MD, as compared to their ideal values.

Now, the question is, are there ideal values for these parameters?

For example, is it reasonable to assume that the ideal values for roll, slide, twist and rise are 0, 0, 36 and 3.4, respectively.

What about shift and tilt, is it reasonable to assume that their ideal values are zero?

Thanks
Miguel

[xiangjun]

Having never performed MD simulations, I am not sure how an idealized uniform structure would effect your comparisons. With 3DNA, you can build a structure with any prescribed step parameters. However, the backbone geometry would normally be distorted, especially at the connections between nucleotides.

What initial structure do you start with for your MD? Can't it be used for your comparison? How about fiber B-form DNA? Any comments from MD experts?

Xiang-Jun