Rodrigo Faccioli wrote:
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.
If you're after a single-point energy, then a zero-step MD is better than a
one-step EM, which will, by its nature, try to change your coordinates.
The reason (I think) for all the present difficulties is because your
coordinates are unreasonable. Have you looked at "2.pdb" in, i.e. VMD? The
coordinates make no sense, with atoms overlapping each other everywhere. It is
for this reason that mdrun basically fails and writes a bad .edr file.
-Justin
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.abra...@anu.edu.au
<mailto:mark.abra...@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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--
========================================
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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