AMBER Archive (2008)

Subject: AMBER: segmentation fault while generating the covariance matrix

From: rams rams (
Date: Tue Feb 05 2008 - 23:12:29 CST

Dear Amber users,

I am trying to generate a covariance matrix (to do PCA) and subsequently
diagonalization using ptraj. After checking the coordinates of all the crd
files supplied, it complains like "segmentation fault" and the program
terminates. The following are the commands I am using to generate the
covariance matrix. Please correct me if I am making any mistake also let me
know what is the upper limit for vecs. The following is the script I am

trajin .crd

matrix covar name mcovar out mcovar.dat
analyze matrix mcovar out evec.pev vecs 10

I am executing this with the following command:

ptraj .top <.trajin> .out

I am loading 20 crd files in this.

Thanks and Regards,

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