AMBER Archive (2006)

Subject: Re: AMBER: ptraj distance matrix

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Wed Jan 11 2006 - 02:09:33 CST


Am Dienstag, 10. Januar 2006 23:03 schrieb Holly Freedman:
> hi AMBER help,
>
> I ran the following command in ptraj:
>
> trajin ../traj
> matrix dist @1-624 out distances
>
> I was expecting to get a matrix of interatomic distances for each atom
> in the specified mask and each frame in the trajectory, but I got only
> one matrix for each atom in the mask. Is ptraj averaging these
> distances over all frames in the trajectory? (This would be nice in fact
> for my purpose)

Yes, you get the average as output.

Best regards

Holger

>
> Thanks,
> --Holly
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-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Juniorprofessur fuer Molekulare Bioinformatik

J.W. Goethe-Universitaet Fachbereich Biowissenschaften Institut für Zellbiologie und Neurowissenschaft Marie-Curie-Str. 9 60439 Frankfurt/Main Germany

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