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, < [email protected]> 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. > -- > 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 [email protected]. > -- 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 [email protected].
