[gmx-users] Gromacs error

Budheswar Dehury bude at kemi.dtu.dk
Wed May 29 14:11:12 CEST 2019

Dear GROMACS Developers and users,

While trying to clustering analysis based on certain distance matrices, however, while trying to perform PCA, I executed the following command, it shows the following error. Need your valuable suggestion and feedback to get rid of such errors.

Thanking you

gmx covar -f pca.xtc -s pca_dummy.pdb -nofit -nomwa -nopbc
                      :-) GROMACS - gmx covar, 2019.2 (-:

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GROMACS:      gmx covar, version 2019.2
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /home/bd422/Desktop/BD/1
Command line:
  gmx covar -f pca.xtc -s pca_dummy.pdb -nofit -nomwa -nopbc

WARNING: Masses and atomic (Van der Waals) radii will be guessed
         based on residue and atom names, since they could not be
         definitively assigned from the information in your input
         files. These guessed numbers might deviate from the mass
         and radius of the atom type. Please check the output
         files if necessary.

Choose a group for the covariance analysis
Group     0 (         System) has 66506 elements
Group     1 (        Protein) has 66506 elements
Group     2 (      Protein-H) has 66506 elements
Group     3 (        C-alpha) has 66506 elements
Group     4 (       Backbone) has 66506 elements
Group     5 (      MainChain) has 66506 elements
Group     6 (   MainChain+Cb) has 66506 elements
Group     7 (    MainChain+H) has 66506 elements
Group     8 (      SideChain) has     0 elements
Group     9 (    SideChain-H) has     0 elements
Select a group: 0
Selected 0: 'System'

Program:     gmx covar, version 2019.2
Source file: src/gromacs/utility/smalloc.cpp (line 125)

Fatal error:
Not enough memory. Failed to calloc 39807432324 elements of size 4 for mat
(called from file
/home/bd422/Downloads/gromacs-2019.2/src/gromacs/gmxana/gmx_covar.cpp, line

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

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