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.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
