[gmx-users] Gromacs error

[Budheswar Dehury]

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
Budheswar

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

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
 Christian Wennberg    Maarten Wolf
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

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
260)

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