[gmx-developers] gmx_d nmeig command Not enough memory

Adrien Nicolaï adrien.nicolai at u-bourgogne.fr
Tue Jul 5 14:08:39 CEST 2016

Dear GROMACS developers,

I’m performing a Normal mode analysis using the GROMACS 5.1 software. The system I study is a dimer of a protein surrounded by water molecules and is comprised of 21075 atoms (corresponding to 63225 modes). After a proper minimisation using the L-BFGS algorithm and a normal mode calculation in double precision, I tried to diagonalise the entire hessian matrix using the nmeig command.

The use of the gmx_d nmeig command leads to the following error:

Reading double precision matrix generated by GROMACS VERSION 5.1

Program gmx nmeig, VERSION 5.1
Source code file: /tmp3/gromacs-5.1-20150825/gromacs-5.1/src/gromacs/utility/smalloc.c, line: 182

Fatal error:
Not enough memory. Failed to calloc -297566671 elements of size 8 for eigenvectors
(called from file /tmp3/gromacs-5.1-20150825/gromacs-5.1/src/gromacs/gmxana/gmx_nmeig.c, line 401)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors <http://www.gromacs.org/Documentation/Errors>
: Cannot allocate memory
Using begin = 1 and end = 63225
Sparse matrix storage format, nrow=63225, ncols=63225
Starter(339849): Return code=1
Starter end(339849)

Could you help me with the meaning of this error? Is my system to big for NMA using GROMACS 5.1?

Thanks you in advance for your help

Best regards,

Adrien Nicolaï / Maître de conférences
Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS
Département NANO - Equipe Physique appliquée aux protéines
Université de Bourgogne Franche-Comté / Faculté des Sciences et Techniques Mirande
9, Av. Savary - B.P. 47 870 21078. DIJON CEDEX - France
Email : adrien.nicolai at u-bourgogne.fr <mailto:adrien.nicolai at u-bourgogne.fr>
Tél: 03 80 39 60 93
URL : https://icb.u-bourgogne.fr/fr/axes-scientifiques/nano/physique-appliquee-aux-proteines.html <https://icb.u-bourgogne.fr/fr/axes-scientifiques/nano/physique-appliquee-aux-proteines.html>

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