[gmx-users] Gromacs error

Dallas Warren dallas.warren at monash.edu
Wed May 29 23:37:55 CEST 2019

Has the following note (as does 'gmx help covar'):
"Note that the diagonalization of a matrix requires memory and time
that will increase at least as fast as than the square of the number
of atoms involved. It is easy to run out of memory, in which case this
tool will probably exit with a ‘Segmentation fault’. You should
consider carefully whether a reduced set of atoms will meet your needs
for lower costs."

Plus see http://www.gromacs.org/Documentation/Errors#Cannot_allocate_memory

So it appears that the system size is too large to be able to perform
the calculation with the computer memory that you have available.  See
last link for suggestions on how to solve.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Wed, 29 May 2019 at 22:11, Budheswar Dehury <bude at kemi.dtu.dk> wrote:
> 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
> --
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