AMBER Archive (2005)

Subject: Re: AMBER: calculating end-end distance

From: David A. Case (case_at_scripps.edu)
Date: Tue Nov 15 2005 - 10:24:01 CST

On Tue, Nov 15, 2005, C Balasubramanian wrote:
>
> I have a trajectory file having around 5000 frames. The MD was done on 12
> mer DNA duplex. I want to calculate the end-end distance over all these
> frames to check the variations during MD. It would be highly helpful if
> someone could tell me whether i can do it with Ptraj or if there is any
> software which can do this calculation.

ptraj has a "distance" command that will compute the distance between any pair
of atoms. If you choose a pair at the top and the bottom of the structure,
that should give you what you want.

...good luck..dac

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