Index of a Hessian matrix

[Alexander Fokas]

Hello,

If I want to analyse my own hessian matrix in the nma analysis, what will the index of the hessian matrix need to be?

Many thanks,

Alexander

[Lars Skjærven]

Hi Alexander, The hessian is a 3Nx3N matrix with atom blocks located at positions with indices ((3i-2):(3i), ((3j-2):(3j)) for atoms (i, j) (e.g. (1:3, 4:6) for atoms (1, 2)).

# read pdb and build hessian
pdb = read.pdb("1etl")
a = trim(pdb, "calpha", resno=5:7)
h = build.hessian(a$xyz, pfc.fun=load.enmff())

# atom 1
> h[1:3, 1:3]
          [,1]      [,2]      [,3]
[1,]  102.8695 -199.5620 -201.0667
[2,] -199.5620  387.1411  390.0600
[3,] -201.0667  390.0600  393.0010

# fc between atom 1 and 2
> h[1:3, 4:6]
          [,1]      [,2]      [,3]
[1,] -102.8695  199.5620  201.0667
[2,]  199.5620 -387.1411 -390.0600
[3,]  201.0667 -390.0600 -393.0010

hope this helps