[gmx-users] covariance map for all residues

[marzieh dehghan]

Hi
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
covara.xpm

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.*