[gmx-users] concatenate tpr files for PCA analysis

Prasanth G, Research Scholar prasanthghanta at sssihl.edu.in
Fri Apr 19 08:27:53 CEST 2019

Dear all,

I am interested in carrying out pca analysis of protein with ligand
(complex). I had carried out a simulation for 20 ns and extended it by 10
ns (making it a 30ns simulation).
I had extracted protein trajectories from both the simulations and joined
them together using -cat flag.

I observed that in some cases, people perform the analysis with a pdb or a
gro file (snapshot dumped at 0ns) of the protein. But gmx gives a warning
stating that the part of protein that has moved out of the box cannot be
recovered. This made me choose tpr file as a reference.
When i try to run the gmx covar with 20ns tpr file as reference using the
below command,

$ gmx_mpi covar -s protein_center_0_20.tpr -f protein_center_0_30.xtc -xpma

I get a note like this,

Note: the fit and analysis group are identical,
      while the fit is mass weighted and the analysis is not.
      Making the fit non mass weighted.

Calculating the average structure ...
Reading frame    2000 time 20000.000
Constructing covariance matrix (1314x1314) ...
Reading frame    2000 time 20000.000
Read 3002 frames

Trace of the covariance matrix: 27.4516 (nm^2)
Diagonalizing ...

Sum of the eigenvalues: 27.4516 (nm^2)

Writing eigenvalues to eigenval.xvg

Writing reference, average structure & eigenvectors 1--1314 to eigenvec.trr
Wrote the log to covar.log

It looks like, gmx only considers the 2000 frames (20ns) for analysis. I
would be grateful if someone can help me in this regard.


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