[gmx-users] concatenate tpr files for PCA analysis

[Mark Abraham]

Hi,

What does gmx dump say about the contents of your xtc file?

Mark

On Fri., 19 Apr. 2019, 08:29 Prasanth G, Research Scholar, <
prasanthghanta at sssihl.edu.in> wrote:

> 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
> covar.xpm
>
> 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)
> 100%
> 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.
>
> --
> Regards,
> Prasanth.
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