[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
> >  > >
> >  > > 
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> >  > --
> >  > ========================================
> >  >
> >  > Justin A. Lemkul
> >  > Graduate Research Assistant
> >  > ICTAS Doctoral Scholar
> >  > Department of Biochemistry
> >  > Virginia Tech
> >  > Blacksburg, VA
> >  > jalemkul[at]vt.edu | (540) 231-9080
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> -- 
> ========================================
> 
> 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
> 
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