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

[Arneh Babakhani]

Hello, I'm experiencing the exact same problem, when trying to do some 
restrained molecular dynamics of a small peptide in a water box. Have 
you had any luck in trouble-shooting this? (I've pasted my mdp file 
below, for your reference).  Also running Gromacs 3.3.1

Arneh

title = ResMD
warnings = 10
cpp = /usr/bin/cpp ; location of cpp on SGI
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 25000 ; total 50.0 ps.
nstcomm = 1
nstxout = 500 ; output coordinates every 1.0 ps
nstvout = 1000 ; output velocities every 2.0 ps
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = berendsen
tau_t = 0.1 0.1
tc_grps = protein sol
ref_t = 300 300
; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529

Diane Fournier wrote:
>  
>
> ________________________________
>
> De: gmx-users-bounces at gromacs.org de la part de David van der Spoel
> Date: lun. 2006-05-01 13:33
> À: Discussion list for GROMACS users
> Objet : Re: [gmx-users] segmentation fault in mdrun when using PME
>
>
>
>
> Have you enabled fortran at the compilation stage? In that case try it
> without, otherwise please file a bugzilla, such that we can document
> this problem (and try to fix it of course).
>
>   
>> Still doesn't work. logfile ends in the usual way. Except this time, I get this output:
>>
>>     
>
> Reading file trp_em.tpr, VERSION 3.3.1 (single precision)
>
> Steepest Descents:
>
> Tolerance (Fmax) = 1.00000e+03
>
> Number of steps = 500
>
> Warning: 1-4 interaction between 1 and 7 at distance 39513.957 which is larger than the 1-4 table size 1.000 nm
>
> These are ignored for the rest of the simulation
>
> This usually means your system is exploding,
>
> if not, you should increase table-extension in your mdp file
>
> Wrote pdb files with previous and current coordinates
>
> Back Off! I just backed up step0.pdb to ./#step0.pdb.1#
>
> Wrote pdb files with previous and current coordinates
>
> and then these files get written:
>
> step0.pdb
>
> #step0.pdb.1# 
>
> step-1.pdb 
>
> step1.pdb 
>
> Will file a bugzilla.
>   
>>>
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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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