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MD simulations / Re: Average or Global properties from a simulation
« on: March 24, 2017, 07:45:55 am »
Dear Xiang-Jun

Thank you very much for your replies. I ended up using some scripts to calculate a distribution of zp values over the simulation time. This will suffice for the time being !



MD simulations / Average or Global properties from a simulation
« on: March 23, 2017, 08:10:57 am »
Dear All

I am trying to extract some average properties from a 30-residue RNA duplex to distinguish between the A or the B form from a trajectory. I read the paper referenced by the admin earlier, but cannot find the documentation to extract the zp value or its distribution.

The second question pertains to extracting average (averaged over all base pairs) global properties over the entire double helix. Although this can be achieved with some additional scripts, I was hoping that there was already such an option present, so that one could extract, for example, the average radius of the helix (plusminus fluctuation), or the average zp parameter. Is there a user manual for 3DNA in place? I found the one for DSSR, but not 3DNA

Thank you in advance for the help, and I hope that I have not simply "not read the manual".


MD simulations / Re: A-Form B-Form RNA/DNA
« on: March 23, 2017, 07:53:55 am »
Dear All

Where exactly is the output for Zp written? I was unable to find a user manual or specific documentation.

Thank you !

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.