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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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