[gmx-users] Unexplained crashes with Gromacs-4.0

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 14 13:19:45 CEST 2008 


Berk Hess wrote:
> Hi,
> 
> I don't really know what could be the problem here.
> 
> 0..180 is (confusingly) not including the end, so 180 is out of range.
> 
> The only thing I can think of (except for unknown bugs of coarse),
> is that I corrected the coupling time of the Parrinello-Rahman barostat
> when going from 4.0 RC4 to the official 4.0 release.
> I guess all your old simulations were with older Gromacs releases.
> So to get the same coupling as before, so would need to multiply tau_t 
> by 16.6.
> I don't know if this would help.

I did see this same error under RC2, but noticed that you fixed this bug shortly 
after I saw it, and that's what I assumed it was.  But now I have seen it under 
the official 4.0 release.

> 
> You did not get pressure coupling warnings before the crash?
> 

There are no messages printed before this error pops up.  What's really 
confusing is that if I simply try the same .tpr file again, it runs without a 
problem.  I know that's not terribly scientific, but it seemed odd to me that my 
systems running for 40+ ns suddenly had a problem.

Is there any diagnostic information I can provide?  This problem seems like it 
would be elusive, since even I can't fully reproduce it.

-Justin

> Berk
> 
> 
> ------------------------------------------------------------------------
>  > Date: Mon, 13 Oct 2008 16:55:20 -0400
>  > From: jalemkul at vt.edu
>  > To: gmx-users at gromacs.org
>  > Subject: [gmx-users] Unexplained crashes with Gromacs-4.0
>  >
>  >
>  > Hi,
>  >
>  > I've gotten the following error with two of my simulation systems. 
> Usually this
>  > weird "variable ci" error means the system is unstable, and I've seen 
> it before
>  > when I've done a poor job of equilibrating. But now I'm seeing it a 
> long time
>  > into my simulations (after 48 ns in one case, 60 ns in the other). If 
> I simply
>  > re-submit the job, it runs fine. The error shown is as follows:
>  >
>  > -------------------------------------------------------
>  > Program mdrun_4.0_mpi, VERSION 4.0
>  > Source code file: nsgrid.c, line: 357
>  >
>  > Range checking error:
>  > Explanation: During neighborsearching, we assign each particle to a grid
>  > based on its coordinates. If your system contains collisions or parameter
>  > errors that give particles very high velocities you might end up with 
> some
>  > coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
>  > put these on a grid, so this is usually where we detect those errors.
>  > Make sure your system is properly energy-minimized and that the potential
>  > energy seems reasonable before trying again.
>  >
>  > Variable ci has value 180. It should have been within [ 0 .. 180 ]
>  >
>  > -------------------------------------------------------
>  >
>  > It seems to me that this "ci" variable is still within the range of 
> 0->180, if
>  > those values are inclusive.
>  >
>  > My .mdp file is as follows:
>  >
>  > title = NPT simulation for a membrane protein
>  > ; Run parameters
>  > integrator = md
>  > dt = 0.002
>  > nsteps = 5000000 ; 10000 ps (10 ns)
>  > tinit = 40000
>  > nstcomm = 1
>  > ; Output parameters
>  > nstxout = 50000 ; every 100 ps
>  > nstvout = 50000
>  > nstfout = 50000
>  > nstlog = 5000 ; every 10 ps
>  > nstenergy = 5000
>  > nstxtcout = 5000
>  > ; Bond parameters
>  > constraint_algorithm = lincs
>  > constraints = all-bonds
>  > continuation = yes
>  > ; Cut-off's and neighborsearching
>  > nstlist = 5
>  > ns_type = grid
>  > rlist = 1.2
>  > rcoulomb = 1.2
>  > rvdw = 1.2
>  > ; PME electrostatics parameters
>  > coulombtype = PME
>  > fourierspacing = 0.18
>  > ;fourier_nx = 0
>  > ;fourier_ny = 0
>  > ;fourier_nz = 0
>  > pme_order = 4
>  > ewald_rtol = 1e-5
>  > optimize_fft = yes
>  > ; Berendsen temperature coupling is on in three groups
>  > Tcoupl = Nose-Hoover
>  > tc_grps = Protein POPC SOL_NA+_CL-
>  > tau_t = 0.1 0.1 0.1
>  > ref_t = 310 310 310
>  > ; Pressure coupling is not on
>  > Pcoupl = Parrinello-Rahman
>  > pcoupltype = semiisotropic
>  > tau_p = 2.0
>  > compressibility = 4.5e-5 4.5e-5
>  > ref_p = 1.0 1.0
>  > ; Generate velocities is off
>  > gen_vel = no
>  > gen_temp = 310
>  > gen_seed = 7041776
>  > ; Periodic boundary conditions are on in all directions
>  > pbc = xyz
>  > ; Long-range dispersion correction
>  > DispCorr = EnerPres
>  >
>  > Any ideas what's going on?
>  >
>  > Thanks,
>  > Justin
>  >
>  > --
>  > ========================================
>  >
>  > Justin A. Lemkul
>  > Graduate Research Assistant
>  > 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
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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