<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"><HTML DIR=ltr><HEAD><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1"></HEAD><BODY><DIV><FONT face='Arial' color=#000000 size=2>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.</FONT><FONT face=Arial
size=2> </FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>I'm working with Gromacs v. 3.3.1 on a
SGI altix 3700 with 32 Intel Itanium</FONT> 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).</DIV>
<DIV> </DIV>
<DIV>the em.mdp file looks like:</DIV>
<DIV> </DIV>
<DIV><FONT face="Courier New"
size=2>title
=
drg_trp<BR>cpp
=
/usr/bin/cpp<BR>define
=
-DFLEX_SPC<BR>constraints
= none<BR>integrator
=
steep<BR>dt
= 0.002 ; ps
!<BR>nsteps
=
500<BR>nstlist
=
10<BR>ns_type
=
grid<BR>rlist
=
0.9<BR>coulombtype
=
PME<BR>rcoulomb
=
0.9<BR>rvdw
=
0.9<BR>fourierspacing
=
0.12<BR>fourier_nx
=
0<BR>fourier_ny
=
0<BR>fourier_nz
=
0<BR>pme_order
=
4<BR>ewald_rtol
=
1e-5<BR>optimize_fft
= yes<BR>;<BR>; Energy minimizing
stuff<BR>;<BR>emtol
=
1000.0<BR>emstep
= 0.01<BR></FONT></DIV>
<DIV><FONT face="Courier New" size=2><FONT face="Times New Roman" size=3>Is it
possible this could be related to insufficient memory allocation ? How demanding
is this PME calculation ?</FONT></DIV></FONT>
<DIV> </DIV></BODY></HTML>