GROMACS version: 2018.6
GROMACS modification: No
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Hi, I have done PCA on the backbone trajectory from a protein simulation using gmx covar and gmx anaeig.
But how do we extract the movie of the entire protein’s motion along the first two principal components from the PCA done on backbone trajectory?
So what I generally do is:
I have a protein structure file protein.gro and trajectory file protein.xtc, Iet’s say I extract backbone.gro and backbone.xtc and now do the following:
gmx covar -s backbone.gro -f backbone.xtc -o WT_eigenval_bb.xvg -v WT_eigenvec_bb.trr
gmx anaeig -s backbone.gro -f backbone.xtc -v WT_eigenvec_bb.trr -2d WT_pca_2d.xvg -filt backbone_reduced.xtc -first 1 -last 2
This gives the movie of the backbone, but how do I get the movie of the whole protein along the first two eigenvectors. What I thought was to project the protein.xtc along the first two eigenvectors derived from the backbone motion like this:
gmx anaeig -s protein.gro -f protein.xtc -v WT_eigenvec_bb.trr -2d WT_ protein _pca_2d.xvg -filt protein_reduced.xtc -first 1 -last 2
Can you please let me know if this is right?
PS note: the gromacs commands are inspired from the discussion of user: minghao2121