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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Nov 15 2005 - 16:53:00 PST
