[gmx-users] concatenate tpr files for PCA analysis

Subhomoi Borkotoky subhomoy.bk at gmail.com
Sat Apr 20 03:17:01 CEST 2019


Hi,

When you extended the simulation from 20ns to 30ns you must've created one
new tpr file.  Use that with your 30ns xtc.

On Fri, Apr 19, 2019, 11:59 AM 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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