Hi,
> I want to calculate the distance between the N1 atom of GUA 61 and
[...]
> between 2 .6A and 4A in 300kand 400k. But in fact, the distance will
> beyond 5A could you help me how to do that .
Your script looks fine to me. Why do you think the distance should be >5A?
Are you comparing to experiment, to your expectation or to some other
simulation? You could use e.g. VMD to visualize the trajectory and
doublecheck how large the distance really is, but I doubt that ptraj will
calculate this value incorrectly.
Kind Regards,
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Thu Aug 11 2011 - 01:30:03 PDT
