[gmx-users] gmx covar error in gromacs2019.x

Mon Jan 6 09:52:22 CET 2020

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&nbsp; &nbsp; &nbsp;0 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;System) has 124748 elements
Group&nbsp; &nbsp; &nbsp;1 (&nbsp; &nbsp; &nbsp; &nbsp; Protein) has&nbsp; 8851 elements
Group&nbsp; &nbsp; &nbsp;2 (&nbsp; &nbsp; &nbsp; Protein-H) has&nbsp; 4419 elements
Group&nbsp; &nbsp; &nbsp;3 (&nbsp; &nbsp; &nbsp; &nbsp; C-alpha) has&nbsp; &nbsp;574 elements
Group&nbsp; &nbsp; &nbsp;4 (&nbsp; &nbsp; &nbsp; &nbsp;Backbone) has&nbsp; 1722 elements
Group&nbsp; &nbsp; &nbsp;5 (&nbsp; &nbsp; &nbsp; MainChain) has&nbsp; 2298 elements
Group&nbsp; &nbsp; &nbsp;6 (&nbsp; &nbsp;MainChain+Cb) has&nbsp; 2824 elements
Group&nbsp; &nbsp; &nbsp;7 (&nbsp; &nbsp; MainChain+H) has&nbsp; 2852 elements
Group&nbsp; &nbsp; &nbsp;8 (&nbsp; &nbsp; &nbsp; SideChain) has&nbsp; 5999 elements
Group&nbsp; &nbsp; &nbsp;9 (&nbsp; &nbsp; SideChain-H) has&nbsp; 2121 elements
Group&nbsp; &nbsp; 10 (&nbsp; &nbsp; Prot-Masses) has&nbsp; 8851 elements
Group&nbsp; &nbsp; 11 (&nbsp; &nbsp; non-Protein) has 115897 elements
Group&nbsp; &nbsp; 12 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Other) has&nbsp; &nbsp; 23 elements
Group&nbsp; &nbsp; 13 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; MOL) has&nbsp; &nbsp; 23 elements
Group&nbsp; &nbsp; 14 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;NA) has&nbsp; &nbsp; &nbsp;8 elements
Group&nbsp; &nbsp; 15 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Water) has 115866 elements
Group&nbsp; &nbsp; 16 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; SOL) has 115866 elements
Group&nbsp; &nbsp; 17 (&nbsp; &nbsp; &nbsp; non-Water) has&nbsp; 8882 elements
Group&nbsp; &nbsp; 18 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Ion) has&nbsp; &nbsp; &nbsp;8 elements
Group&nbsp; &nbsp; 19 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; MOL) has&nbsp; &nbsp; 23 elements
Group&nbsp; &nbsp; 20 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;NA) has&nbsp; &nbsp; &nbsp;8 elements
Group&nbsp; &nbsp; 21 ( Water_and_ions) has 115874 elements
Group&nbsp; &nbsp; 22 (&nbsp; &nbsp; Protein_lig) has&nbsp; 8874 elements
Group&nbsp; &nbsp; 23 (center_Val108_A) has&nbsp; &nbsp; 16 elements
Group&nbsp; &nbsp; 24 (&nbsp; &nbsp; &nbsp; &nbsp; chain_A) has&nbsp; 4427 elements
Group&nbsp; &nbsp; 25 (&nbsp; &nbsp; &nbsp; &nbsp; chain_B) has&nbsp; 4424 elements
Group&nbsp; &nbsp; 26 (C-alpha_&amp;_chain_A) has&nbsp; &nbsp;287 elements
Group&nbsp; &nbsp; 27 (C-alpha_&amp;_chain_B) has&nbsp; &nbsp;287 elements
Group&nbsp; &nbsp; 28 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; E53) has&nbsp; &nbsp; 15 elements
Group&nbsp; &nbsp; 29 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;K135) has&nbsp; &nbsp; 22 elements
Group&nbsp; &nbsp; 30 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;C169) has&nbsp; &nbsp; 11 elements
Group&nbsp; &nbsp; 31 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; S) has&nbsp; &nbsp; &nbsp;1 elements
Group&nbsp; &nbsp; 32 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; C13) has&nbsp; &nbsp; &nbsp;1 elements
Select a group: Selected 3: 'C-alpha'

Choose a group for the covariance analysis
Group&nbsp; &nbsp; &nbsp;0 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;System) has 124748 elements
Group&nbsp; &nbsp; &nbsp;1 (&nbsp; &nbsp; &nbsp; &nbsp; Protein) has&nbsp; 8851 elements
Group&nbsp; &nbsp; &nbsp;2 (&nbsp; &nbsp; &nbsp; Protein-H) has&nbsp; 4419 elements
Group&nbsp; &nbsp; &nbsp;3 (&nbsp; &nbsp; &nbsp; &nbsp; C-alpha) has&nbsp; &nbsp;574 elements
Group&nbsp; &nbsp; &nbsp;4 (&nbsp; &nbsp; &nbsp; &nbsp;Backbone) has&nbsp; 1722 elements
Group&nbsp; &nbsp; &nbsp;5 (&nbsp; &nbsp; &nbsp; MainChain) has&nbsp; 2298 elements
Group&nbsp; &nbsp; &nbsp;6 (&nbsp; &nbsp;MainChain+Cb) has&nbsp; 2824 elements
Group&nbsp; &nbsp; &nbsp;7 (&nbsp; &nbsp; MainChain+H) has&nbsp; 2852 elements
Group&nbsp; &nbsp; &nbsp;8 (&nbsp; &nbsp; &nbsp; SideChain) has&nbsp; 5999 elements
Group&nbsp; &nbsp; &nbsp;9 (&nbsp; &nbsp; SideChain-H) has&nbsp; 2121 elements
Group&nbsp; &nbsp; 10 (&nbsp; &nbsp; Prot-Masses) has&nbsp; 8851 elements
Group&nbsp; &nbsp; 11 (&nbsp; &nbsp; non-Protein) has 115897 elements
Group&nbsp; &nbsp; 12 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Other) has&nbsp; &nbsp; 23 elements
Group&nbsp; &nbsp; 13 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; MOL) has&nbsp; &nbsp; 23 elements
Group&nbsp; &nbsp; 14 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;NA) has&nbsp; &nbsp; &nbsp;8 elements
Group&nbsp; &nbsp; 15 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Water) has 115866 elements
Group&nbsp; &nbsp; 16 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; SOL) has 115866 elements
Group&nbsp; &nbsp; 17 (&nbsp; &nbsp; &nbsp; non-Water) has&nbsp; 8882 elements
Group&nbsp; &nbsp; 18 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Ion) has&nbsp; &nbsp; &nbsp;8 elements
Group&nbsp; &nbsp; 19 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; MOL) has&nbsp; &nbsp; 23 elements
Group&nbsp; &nbsp; 20 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;NA) has&nbsp; &nbsp; &nbsp;8 elements
Group&nbsp; &nbsp; 21 ( Water_and_ions) has 115874 elements
Group&nbsp; &nbsp; 22 (&nbsp; &nbsp; Protein_lig) has&nbsp; 8874 elements
Group&nbsp; &nbsp; 23 (center_Val108_A) has&nbsp; &nbsp; 16 elements
Group&nbsp; &nbsp; 24 (&nbsp; &nbsp; &nbsp; &nbsp; chain_A) has&nbsp; 4427 elements
Group&nbsp; &nbsp; 25 (&nbsp; &nbsp; &nbsp; &nbsp; chain_B) has&nbsp; 4424 elements
Group&nbsp; &nbsp; 26 (C-alpha_&amp;_chain_A) has&nbsp; &nbsp;287 elements
Group&nbsp; &nbsp; 27 (C-alpha_&amp;_chain_B) has&nbsp; &nbsp;287 elements
Group&nbsp; &nbsp; 28 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; E53) has&nbsp; &nbsp; 15 elements
Group&nbsp; &nbsp; 29 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;K135) has&nbsp; &nbsp; 22 elements
Group&nbsp; &nbsp; 30 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;C169) has&nbsp; &nbsp; 11 elements
Group&nbsp; &nbsp; 31 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; S) has&nbsp; &nbsp; &nbsp;1 elements
Group&nbsp; &nbsp; 32 (&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; C13) has&nbsp; &nbsp; &nbsp;1 elements
Select a group: Selected 3: 'C-alpha'
Calculating the average structure ...
Reading frame&nbsp; &nbsp; &nbsp; &nbsp;0 time&nbsp; &nbsp; 0.000&nbsp; &nbsp;
WARNING: number of atoms in tpx (574) and trajectory (8851) do not match
Last frame&nbsp; &nbsp; &nbsp; 10000 time&nbsp;100000.000&nbsp; &nbsp;

Back Off! I just backed up average.pdb to ./#average.pdb.3#
Constructing covariance matrix (1722x1722) ...
Last frame&nbsp; &nbsp; &nbsp; 10000 time&nbsp;100000.000&nbsp; &nbsp;
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:&nbsp; &nbsp; &nbsp;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&nbsp;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 &amp;&amp; cd cmake-*
./bootstrap
gmake &amp;&amp; gmake install
yum remove cmake -y
ln -s /usr/local/bin/cmake /usr/bin/

fftw-3.3.8
tar -zxvf fftw* &amp;&amp; cd fftw*
./configure --prefix=/usr/local/fftw3.3.8 --enable-sse2 --enable-avx&nbsp; --enable-avx2 --enable-float --enable-shared
make install -j 16

gmx2019.4
&nbsp; &nbsp; tar xfz gromacs-2019.4.tar.gz &amp;&amp; cd gromacs-2019.4
&nbsp; &nbsp; mkdir build &amp;&amp; cd build
&nbsp; &nbsp; export CMAKE_PREFIX_PATH=/usr/local/fftw3.3.8

&nbsp; &nbsp; cmake .. -DCMAKE_INSTALL_PREFIX=/opt/software/gmx2019.4 -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-10.2
&nbsp; &nbsp; make -j 16
&nbsp; &nbsp; make check
&nbsp; &nbsp; make install

Thanks in advance.
Regards