[gmx-users] Unexplained crashes with Gromacs-4.0

[Berk Hess]

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.

You did not get pressure coupling warnings before the crash?

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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