[gmx-users] (no subject)
Antonia V.
antonia_haha at hotmail.com
Wed Apr 1 18:44:32 CEST 2009
I switched to v-rescale for the thermostat and things look normal!
Thanks for the help
Antonia
> Date: Wed, 1 Apr 2009 12:11:47 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] (no subject)
>
>
>
> Antonia V. wrote:
> > > 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
> >
>
> Your potential energy has spiked to a very large value. That indicates you
> still have some bad contacts in the system.
>
> > > 3. What happened in the EM procedure?
> > After the EM (steep) the forces were minimized to the desired accuracy
> > (Tolerance (Fmax) = 1.00000e+02)
> >
>
> Was the potential reasonable? See above.
>
> > > 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)
> >
>
> Well, these are not all of your parameters, surely (it's best to post your whole
> .mdp file). If you are going for 340 K, you can see from your .log file that
> the temperature is actually 0.34 K. Are you doing some sort of annealing
> protocol? Again, it's best to give complete information :)
>
> Nose-Hoover is a poor choice for initial equilibration, if this is what you are
> doing. It allows greater temperature fluctuation. Start with Berendsen or
> V-rescale for some time, then switch to N-H when collecting your "real" data, if
> N-H is your choice for thermostat.
>
> Is a .trr ever output? If it is, you can view the trajectory to see where
> things are going wrong. If you don't get a .trr, then set nstxout = 1 in the
> .mdp file to hopefully get a frame or two of where the problem may lie.
>
> -Justin
>
> > > 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
> >
> > ------------------------------------------------------------------------
> > check out the rest of the Windows Live™. More than mail–Windows Live™
> > goes way beyond your inbox. More than messages
> > <http://www.microsoft.com/windows/windowslive/>
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > 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/20090401/14284f2b/attachment.html>
More information about the gromacs.org_gmx-users
mailing list