Hello I am trying to calculate mass weighted covariance matrix using a Gromacs Topology file <tpr> and a trajectory file <xtc>. The trajectory has only protein coordinates. I am using "gmx_mpi covar" function for the same. I am using following format from the documentation:
gmx_mpi covar -f <traj> -s <topology> -ascii -mwa -b <> -e <> I have tried it both with and without mwa, but in both cases the log file generated says that the analysis is non mass weighted. Does that mean that the covariance matrix is also non mass weighted or not?? With best Regards Tushar Modi Graduate Student Department of Physics Arizona State University -- 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.
