[gmx-users] Error when execute g_energy - the message: not recognized, maybe different CPU?

[Mark Abraham]

On 14/01/2011 12:12 PM, Rodrigo Faccioli wrote:
> Hi,
>
> I have an error when try to execute the g_energy program. I'm using 
> Gromacs 4.5.3 version. My Operation System is Ubuntu 9.10.
>
> Firstly, my apology if my question is basic, but I'm a computer 
> scientist trying to understand the Gromacs concepts for simulation.
>
> My error message appears when I execute the command line: echo '-e' 
> '10' | /usr/local/bin/./g_energy -f 
> /home/faccioli/Execute/EESC_AE/1BDD/energy.edr -o 
> /home/faccioli/Execute/EESC_AE/1BDD/energy.xvg
> -------------------------------------------------------
> Program g_energy, VERSION 4.5.3
> Source code file: /home/faccioli/gromacs-4.5.3/src/gmxlib/enxio.c, 
> line: 772
>
> Fatal error:
> Energy file /home/faccioli/Execute/EESC_AE/1BDD/energy.edr not 
> recognized, maybe different CPU?
> For more information and tips for troubleshooting, please check the 
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ------------------------------------------------------

Does the .edr file have non-zero size? What does gmxcheck have to say 
about it? Does the output of gmxdump show that it has plausible data?

Mark

>
> In [1] contains all files which I used in  my simulation including the 
> energy file (energy.edr) and all commands which I ran 
> (_run_gromacs.txt). The error message appears when try to execute the 
> 2.pdb file. The others (0.pdb and 1.pdb ) I can get the energy value. 
> These pdb files were build using my implementation of Nerf algorithm 
> [2] which converts dihedral angles to Cartesian coordinates.
>
> I looked at line 772  of gmxlib/enxio.c file. However, I didn't 
> understand to fix my problem. I understood my file is not empty, but 
> it is corrupted.  So, I couldn't understand how can it is corrupted.
>
> [1] http://dl.dropbox.com/u/4270818/compute_energy.zip
> [2] http://www.ncbi.nlm.nih.gov/pubmed/15898109
>
> I thanks any help.
>
> --
> Rodrigo Antonio Faccioli
> Ph.D Student in Electrical Engineering
> University of Sao Paulo - USP
> Engineering School of Sao Carlos - EESC
> Department of Electrical Engineering - SEL
> Intelligent System in Structure Bioinformatics
> http://laips.sel.eesc.usp.br
> Phone: 55 (16) 3373-9366 Ext 229
> Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
> Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5