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

[Rodrigo Faccioli]

Thanks for Justin and Mark their answers.

I ran gmxcheck and gmxdump which returned the same error message. Below I
show my command lines and the each error message.

I would like to know if what I'm doing is the better way to obtain the
potential energy of system (protein). I'm asking it because my PhD project
is develop an evolutionary algorithm using Gromacs to compute the energy of
system.

Thanks any help.

Below there are the execution of gmxcheck and gmxdump programs when they
read my energy file:

1) gmxdump -e energy.edr
-------------------------------------------------------
Program gmxdump, VERSION 4.5.3
Source code file: /home/faccioli/gromacs-4.5.3/src/gmxlib/enxio.c, line: 772

Fatal error:
Energy file 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
-------------------------------------------------------

2) gmxcheck -e energy.edr
-------------------------------------------------------
Program gmxcheck, VERSION 4.5.3
Source code file: /home/faccioli/gromacs-4.5.3/src/gmxlib/enxio.c, line: 772

Fatal error:
Energy file 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
-------------------------------------------------------


--
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


On Fri, Jan 14, 2011 at 12:05 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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
>>
>
> --
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