AMBER Archive (2005)

Subject: AMBER: calculating end-end distance

From: C Balasubramanian (cbala_at_igib.res.in)
Date: Tue Nov 15 2005 - 04:24:21 CST

Dear users,

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.

Thanks in advance,
C. Bala

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