[gmx-users] (no subject)

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 1 18:11:47 CEST 2009 


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
>  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  >
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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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