Messages

1

MD simulations / Re: Base stacking from x3dna_ensemble

« on: April 01, 2013, 02:24:30 pm »

Many thanks.

I should've verified by using the trick you noted here.

Regards,

Jung

2

MD simulations / Re: Base stacking from x3dna_ensemble

« on: April 01, 2013, 11:49:04 am »

Dear Xiang-Jun,

Thanks so much for your contribution making the program useful and keeping updated.

I have a follow-up question on this thread.
I wanted to calculate base stacking on a single strand in RNA.  Using the -ring option, I could
extract information of the origin and normal vectors (b1c, b2c, b1n, and b2n)
of each strand following 5' -->3' direction.

After the calculations of distance and angle between bases, I find the distance values make sense, but the angle seems too small.
The equation I use to compute is:
theta  = arccos (dot(n1,n2)) where n1 and n2 are normal vectors from the b1n file

I wonder whether the angle I am getting is in radians?

Regards,

Jung