[gmx-users] (no subject)

[Antonia V.]

> 1. A description of your system

I have a system of 250 5CB molecules (it is a liquid crystal) which means 4750 atoms.

> 2. Anything else that was printed to screen or the .log file (that's where the 
> real error message will appear)

On the screen the message was 
[compute-0-4:01361] *** Process received signal ***
[compute-0-4:01361] Signal: Segmentation fault (11)
[compute-0-4:01361] Signal code: Address not mapped (1)
[compute-0-4:01361] Failing at address: 0x1913c280
[compute-0-4:01361] [ 0] /lib64/libpthread.so.0 [0x32b340de70]
[compute-0-4:01361] [ 1] mdrun [0x6a46cd]
[compute-0-4:01361] *** End of error message ***
Segmentation fault

and the last thing that was written in the md.log file is 

           Step           Time         Lambda
              0        0.00000        0.00000

Grid: 8 x 8 x 8 cells
   Energies (kJ/mol)
           Bond          Angle    Proper Dih.        LJ (SR)   Coulomb (SR)
    3.12078e+03    7.44768e+04    5.19128e+03   -1.67708e+04   -1.07965e+03
   Coul. recip.      Potential    Kinetic En.   Total Energy    Temperature
   -6.75318e+03    5.81852e+04    2.02196e+01    5.82054e+04    3.41383e-01
 Pressure (bar)
   -2.55714e+03

> 3. What happened in the EM procedure?
After the EM (steep) the forces were minimized to the desired accuracy (Tolerance (Fmax)   =  1.00000e+02)

> 4. What .mdp parameters you are using
I use a time step of 2fs, PME for the electrostatics, a quite large cut-off (1.2), the nose-hoover thermostat (340K)

> 5. Which Gromacs version you are using

I use GROMACS 4.0.3 

Thank you 
Antonia

> Date: Wed, 1 Apr 2009 06:39:17 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] (no subject)
> 
> 
> 
> Antonia V. wrote:
> > Hello,
> > 
> > I am trying to simulate a system at the NVT ensemble, but after a few 
> > steps I get the error
> > [compute-0-4:01361] *** Process received signal ***
> > [compute-0-4:01361] Signal: Segmentation fault (11)
> > [compute-0-4:01361] Signal code: Address not mapped (1)
> > [compute-0-4:01361] Failing at address: 0x1913c280
> > [compute-0-4:01361] [ 0] /lib64/libpthread.so.0 [0x32b340de70]
> > [compute-0-4:01361] [ 1] mdrun [0x6a46cd]
> > [compute-0-4:01361] *** End of error message ***
> > Segmentation fault
> > 
> > Any ideas what this means??
> > 
> 
> Given this information, no.  Segmentation faults are difficult to pin down, 
> anyway, but if you want help, you'll have to provide more useful information:
> 
> 1. A description of your system
> 2. Anything else that was printed to screen or the .log file (that's where the 
> real error message will appear)
> 3. What happened in the EM procedure?
> 4. What .mdp parameters you are using
> 5. Which Gromacs version you are using
> 
> -Justin
> 
> > Thank you
> > Antonia
> > 
> > ------------------------------------------------------------------------
> > What can you do with the new Windows Live? Find out 
> > <http://www.microsoft.com/windows/windowslive/default.aspx>
> > 
> > 
> > ------------------------------------------------------------------------
> > 
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_________________________________________________________________
More than messages–check out the rest of the Windows Live™.
http://www.microsoft.com/windows/windowslive/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090401/1c622e60/attachment.html>