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

[Justin A. Lemkul]

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 > 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

Re: [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 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
>>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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www inter

Re: [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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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Re: [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



--


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

[Rodrigo Faccioli]

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.

--
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
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists