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
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 ?
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