# Re: [AMBER] Interpreting the distance covariance matrix

From: Sergio R Aragon <aragons.sfsu.edu>
Date: Tue, 14 Jun 2011 22:16:28 +0000

Hello Sajeewa,

Following up on what Mariano Rech has told you, from 22 carbons atoms you would generate a matrix of distances containing 22^2 = 484 numbers. The number of off-diagonal elements for this symmetric matrix is (484-22)/2 = 231. This is equivalent to the formula n(n-1)/2 that Mariano used. Thus we would believe you have 231 different numbers. That is not at all the same as saying you have a 231 x 231 matrix (that would yield 231^2 = 53 361 numbers!). How many numbers do you actually have?

Cheers,

Sergio Aragon

-----Original Message-----
From: Sajeewa Pemasinghe [mailto:sajeewasp.gmail.com]
Sent: Monday, June 13, 2011 3:49 PM
To: amber.ambermd.org
Subject: [AMBER] Interpreting the distance covariance matrix

Hi,

I have run a distance-covarinace analysis for 22 alpha carbon atoms
specified by the mask1. I thought I would get a 22 by 22 symmetric matrix
where the diagonal elements correspond to the variances. Instead I got a 231
by 231 symmetric matrix. I am having a very hard time interpreting this.
This is my first time running a distance covariance calculation in amber. I
would really appreciate if you could give me some helpful explanation in
interpreting the structure of 231 by 231 matrix.

Best Regards
Sajeewa
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 14 2011 - 15:30:03 PDT
Custom Search
{"ft_lang_label":"__label__en","ft_lang_prob":0.82622904,"math_prob":0.88214874,"size":1550,"snap":"2019-51-2020-05","text_gpt3_token_len":399,"char_repetition_ratio":0.1610608,"word_repetition_ratio":0.018099548,"special_character_ratio":0.3083871,"punctuation_ratio":0.13898306,"nsfw_num_words":0,"has_unicode_error":false,"math_prob_llama3":0.9517864,"pos_list":[0],"im_url_duplicate_count":[null],"WARC_HEADER":"{\"WARC-Type\":\"response\",\"WARC-Date\":\"2020-01-28T00:09:03Z\",\"WARC-Record-ID\":\"<urn:uuid:90ac697d-c80d-4949-aa8e-0161115171b9>\",\"Content-Length\":\"8840\",\"Content-Type\":\"application/http; msgtype=response\",\"WARC-Warcinfo-ID\":\"<urn:uuid:4421b1e1-41c5-4772-a777-11a5f8f31ac7>\",\"WARC-Concurrent-To\":\"<urn:uuid:7ffc46f8-0545-4485-a1b6-ebb42e2d513c>\",\"WARC-IP-Address\":\"192.31.21.165\",\"WARC-Target-URI\":\"http://archive.ambermd.org/201106/0358.html\",\"WARC-Payload-Digest\":\"sha1:QVOJPGXJXQAQBP62DLEP4L74HPU4JFXX\",\"WARC-Block-Digest\":\"sha1:JF6K6J3XYLD5UOQEJTYFP4UT7WPHWPAV\",\"WARC-Identified-Payload-Type\":\"application/xhtml+xml\",\"warc_filename\":\"/cc_download/warc_2020/CC-MAIN-2020-05/CC-MAIN-2020-05_segments_1579251737572.61_warc_CC-MAIN-20200127235617-20200128025617-00004.warc.gz\"}"}