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

[Eduardo Jardón]

Dear Zhang Chen,
In order to calculate the covariance matrix, you have to decide what will
be the reference frame. I suggest play around with option "-ref no/yes".
The reference can be the average coordinates of the C-alpha atoms of the
protein of trajectory 0.pdb. Now, if you changed only the protonation of a
residue in trajectory 1.pdb, the reference can still be the same as
trajectory 0.pdb, but the average of C alpha atoms would not correspond to
the average of the trajectory 1.pdb, so the covariance matrix will be
different from the other 0.pdb trajectory. Often this analysis is done for
a reduced degrees of freedom, like the C alpha, or the dihedral angles, and
rarely for the whole protein including the hydrogen atoms. The main point,
I think, is to decide at what level  would you expect the
protonationated residue would have the major impact. Have you considered to
perform alternative analysis to see first the local local impact ?
>From there you could consider to run secondary structure analysis, side
chains H-bonds, radius of gyration, etc. If you still want to run PCA, you
have to make sure your trajectory is long enough to have  at least two
halves of trajectory 0.pdb CA. 100% overlap of covariance matrices, or
block analysis to calculate overlap error as a function of time length.

best,
Eduardo


El mar., 31 mar. 2020 a las 19:11, ZHANG Cheng (<272699575 at qq.com>)
escribió:

> 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?
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