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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu 

-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
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

Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29464
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://www.uni-frankfurt.de/~hgohlke
++++++++++++++++++++++++++++++++++++++++++++++++++
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu