[gmx-users] segmentation fault in mdrun when using PME

[David van der Spoel]

Diane Fournier wrote:
> Hi, I'm new to Gromacs and I'm trying to run a enzyme-ligand complex 
> molecular dynamics simulation. I have tried doing John 
> Kerrigan's Drug-Enzyme tutorial and mdrun crashes with segmentation 
> fault and core dump at the steepest descents minimization step. However, 
> mdrun works fine when using cutoff instead of PME. 
>  
> I'm working with Gromacs v. 3.3.1 on a SGI altix 3700 with 32 Intel 
> Itanium 2 processors (but I'm currently using a single node, so it's not 
> a MPI problem) under Red Hat Enterprise Linux AS release 3 with Intel 
> Math Kernel Librarary (MKL) v. 8.0.1 as FFT library (which is optimized 
> for Itanium 2).
>  
> the em.mdp file looks like:
>  
> title               =  drg_trp
> cpp                 =  /usr/bin/cpp
> define              =  -DFLEX_SPC
> constraints         =  none
> integrator          =  steep
> dt                  =  0.002    ; ps !
> nsteps              =  500
> nstlist             =  10
> ns_type             =  grid
> rlist               =  0.9
> coulombtype             =  PME
> rcoulomb            =  0.9
> rvdw                =  0.9
> fourierspacing          =  0.12
> fourier_nx              =  0
> fourier_ny              =  0
> fourier_nz              =  0
> pme_order               =  4
> ewald_rtol              =  1e-5
> optimize_fft            =  yes
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  1000.0
> emstep              =  0.01
> Is it possible this could be related to insufficient memory allocation ? 
> How demanding is this PME calculation ?
Not likely a memory problem. It could be a compiler issue but we need 
more info! Where does it crash? Is it reproducible? DOes the same tpr 
file cause a crash on another architecture (e.g. your desktop)?

>  
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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