[gmx-users] covariance map for all residues

marzieh dehghan dehghanmarzieh at gmail.com
Thu Nov 2 18:03:18 CET 2017

Dear all

I want to draw covariance map using gromacs, so I have two questions:

1- I used the following command,but x and y axis show based on atom:

gmx covar -s md.tpr -f md.trr -o eigenval.xvg -v eigenvect.trr -xpma

the number of atoms on the x and y axis is less than total atom numbers in
the pdb files, why is there this conflict?

2- I want to determine covariance map based on residue number, please let
me know which command can I used to solve this problem?

thanks a lot
best wishes

*Marzieh DehghanPhD of BiochemistryInstitute of biochemistry and Biophysics
(IBB)University of Tehran, Tehran- Iran.*

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