[gmx-users] PCA analysis with different atoms in -s and -f

[ZHANG Cheng]

I am trying to compare trajectories from different MD simulations, including different pH and different mutants. The initial PDB (i.e. 0.pdb) is the same, but the derived PDBs (1.pdb, 2.pdb, etc.) are different due to protonation states and mutations. Those different PDBs were used individually for the MD.


To obtain the eigen vectors, should I use the 0.pdb as the reference structure?
# gmx covar -s 0.pdb -f 1.xtc -v 1.trr
(use 0.pdb as reference, and calculate the eigen vectors from trajectories of 1.pdb)


The first is to choose the least squares fit. Though the atoms in "Protein", "Protein-H" are different between 0.pdb and 1.xtc, they are same in "C-alpha", "Backbone" and "MainChain". However, when I choose "C-alpha" for the "least squares fit", I still got the warning:
# WARNING: number of atoms in tpx (442) and trajectory (6622) do not match


The calculation can still be done. So must I provide "1.pdb" as reference for "1.xtc", or is it still okay to use "-s 0.pdb"?


Afterwards, I want to run
# gmx anaeig -s 0.pdb -over overlap_1_2.xvg -v2 1.trr -v 2.trr
to compare the similarity between Condition 1 and Condition 2. Is this correct?