Hi, I am trying to use g_covar like this: echo 2 2 | g_covar -s prod_clus_1_exp.tpr -f prod_clus_exp_fit.xtc -n index_noH_exp.ndx -o eigenval_300K_exp.xvg -v eigenvect_300K_exp.trr
In Gromacs 5.0.4 I get an error: (...) Choose a group for the least squares fit Group 0 ( System) has 4437 elements Group 1 ( Other) has 147 elements Group 2 ( MOL) has 147 elements Select a group: 2 Selected 2: 'MOL' Choose a group for the covariance analysis Group 0 ( System) has 4437 elements Group 1 ( Other) has 147 elements Group 2 ( MOL) has 147 elements Select a group: 2 Selected 2: 'MOL' 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 frames from gro file 'frame t= 18.000', 4437 atoms. Last frame 0 time 18.000 Back Off! I just backed up average.pdb to ./#average.pdb.4# Constructing covariance matrix (441x441) ... Reading frames from gro file 'frame t= 18.000', 4437 atoms. Last frame 0 time 18.000 Read 1 frames Trace of the covariance matrix: 0 (nm^2) Diagonalizing ... Sum of the eigenvalues: 0 (nm^2) Violación de segmento That means "Segmentation fault". The most strange is that using Gromacs 4.6.2 this error does not appear, and the command executes properly. Could it be maybe a bug in Gromacs 5? Thanks a lot for your help in advance. Dr. Rebeca Garcia Santiago de Compostela University (Spain) -- 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.