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

[Justin A. Lemkul]

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
> ------------------------------------------------------
> 
> 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.
> 

It looks like your EM completely failed.  When I ran your input files, I got:

Steepest Descents did not converge to Fmax < 10 in 2 steps.
Potential Energy  =  9.9635511e+10
Maximum force     =  1.7959855e+13 on atom 122
Norm of force     =  2.6216859e+12

This would indicate that perhaps the energy file simply isn't being written 
properly, since the system has basically exploded immediately such that there 
are no viable frames.

-Justin

> --
> 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
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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