Hi gmx users! I am using gmx2019.4 in centos 7.6 (gcc version 4.8.5), the MD was conducted successfully. However, when I proceeded the PCA analysis, there was a wrong in the output informations.
command: echo 3 3|gmx covar -f md_res_center_mol_fit_protein.xtc -s ../md.tpr -o eigenvalues.xvg -v eigenvectors.trr -xpma covapic.xpm -n ../index.ndx output: Choose a group for the least squares fit Group 0 ( System) has 124748 elements Group 1 ( Protein) has 8851 elements Group 2 ( Protein-H) has 4419 elements Group 3 ( C-alpha) has 574 elements Group 4 ( Backbone) has 1722 elements Group 5 ( MainChain) has 2298 elements Group 6 ( MainChain+Cb) has 2824 elements Group 7 ( MainChain+H) has 2852 elements Group 8 ( SideChain) has 5999 elements Group 9 ( SideChain-H) has 2121 elements Group 10 ( Prot-Masses) has 8851 elements Group 11 ( non-Protein) has 115897 elements Group 12 ( Other) has 23 elements Group 13 ( MOL) has 23 elements Group 14 ( NA) has 8 elements Group 15 ( Water) has 115866 elements Group 16 ( SOL) has 115866 elements Group 17 ( non-Water) has 8882 elements Group 18 ( Ion) has 8 elements Group 19 ( MOL) has 23 elements Group 20 ( NA) has 8 elements Group 21 ( Water_and_ions) has 115874 elements Group 22 ( Protein_lig) has 8874 elements Group 23 (center_Val108_A) has 16 elements Group 24 ( chain_A) has 4427 elements Group 25 ( chain_B) has 4424 elements Group 26 (C-alpha_&_chain_A) has 287 elements Group 27 (C-alpha_&_chain_B) has 287 elements Group 28 ( E53) has 15 elements Group 29 ( K135) has 22 elements Group 30 ( C169) has 11 elements Group 31 ( S) has 1 elements Group 32 ( C13) has 1 elements Select a group: Selected 3: 'C-alpha' Choose a group for the covariance analysis Group 0 ( System) has 124748 elements Group 1 ( Protein) has 8851 elements Group 2 ( Protein-H) has 4419 elements Group 3 ( C-alpha) has 574 elements Group 4 ( Backbone) has 1722 elements Group 5 ( MainChain) has 2298 elements Group 6 ( MainChain+Cb) has 2824 elements Group 7 ( MainChain+H) has 2852 elements Group 8 ( SideChain) has 5999 elements Group 9 ( SideChain-H) has 2121 elements Group 10 ( Prot-Masses) has 8851 elements Group 11 ( non-Protein) has 115897 elements Group 12 ( Other) has 23 elements Group 13 ( MOL) has 23 elements Group 14 ( NA) has 8 elements Group 15 ( Water) has 115866 elements Group 16 ( SOL) has 115866 elements Group 17 ( non-Water) has 8882 elements Group 18 ( Ion) has 8 elements Group 19 ( MOL) has 23 elements Group 20 ( NA) has 8 elements Group 21 ( Water_and_ions) has 115874 elements Group 22 ( Protein_lig) has 8874 elements Group 23 (center_Val108_A) has 16 elements Group 24 ( chain_A) has 4427 elements Group 25 ( chain_B) has 4424 elements Group 26 (C-alpha_&_chain_A) has 287 elements Group 27 (C-alpha_&_chain_B) has 287 elements Group 28 ( E53) has 15 elements Group 29 ( K135) has 22 elements Group 30 ( C169) has 11 elements Group 31 ( S) has 1 elements Group 32 ( C13) has 1 elements Select a group: Selected 3: 'C-alpha' Calculating the average structure ... Reading frame 0 time 0.000 WARNING: number of atoms in tpx (574) and trajectory (8851) do not match Last frame 10000 time 100000.000 Back Off! I just backed up average.pdb to ./#average.pdb.3# Constructing covariance matrix (1722x1722) ... Last frame 10000 time 100000.000 Read 10001 frames Trace of the covariance matrix: 9.58344 (nm^2) Back Off! I just backed up covapic.xpm to ./#covapic.xpm.3# 100% Diagonalizing ... ------------------------------------------------------- Program: gmx covar, version 2019.4 Source file: src/gromacs/linearalgebra/eigensolver.cpp (line 137) Fatal error: Internal errror in LAPACK diagonalization. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- I had tested the same files in a virtual machine with centos 7.6 and gmx2019.4 installed, the output was normal and gave the output files I need. Then I used the same files on other server with gmx 4.5.3, and the md.tpr was replaced by md.gro, it was also normal. I had installed gmx2019.2, gmx2019.5 and it gave the same error. the gmx was installed as follows: cmake(version 3.16.0) tar xvf cmake-*.tar.gz && cd cmake-* ./bootstrap gmake && gmake install yum remove cmake -y ln -s /usr/local/bin/cmake /usr/bin/ fftw-3.3.8 tar -zxvf fftw* && cd fftw* ./configure --prefix=/usr/local/fftw3.3.8 --enable-sse2 --enable-avx --enable-avx2 --enable-float --enable-shared make install -j 16 gmx2019.4 tar xfz gromacs-2019.4.tar.gz && cd gromacs-2019.4 mkdir build && cd build export CMAKE_PREFIX_PATH=/usr/local/fftw3.3.8 cmake .. -DCMAKE_INSTALL_PREFIX=/opt/software/gmx2019.4 -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-10.2 make -j 16 make check make install Thanks in advance. Regards -- 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.