[gmx-users] Range checking error

[Yanzi Zhou]

Dear Gromacs-Users,
Is there anybody have met such problem before?

I did NTP simulation for POPE system downloaded from
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies.
It can run for even 10 ns with single precision GROMACS on many
processors or with double precision GROMACS on 1 or 2 processors, but
crash at about 100ps with double
GROMACS on more than 2 processors. The same thing didn't happen for a
NTV simulation.
I don't think it can be ascribed to the initial structure, because I
used the same initial structure and input files for tests. Which one do
you prefer for MD simulation, single or double precision?

Here is the error message:

Program mdrun_mpi_d, VERSION 3.3.2
Source code file: nsgrid.c, line: 226

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value 4421. It should have been within [ 0 .. 4212 ]

-------------------------------------------------------

I compiled GROMACS on Linux x86_64 with mvapich-0.9.9, this is how I
complied it:
#!/bin/csh -f

setenv CC icc
setenv CXX icpc
setenv F77 ifort
setenv MPICC mpicc

setenv CFLAGS "-O3 -fPIC -align -Zp8 -axW -unroll -Wno-deprecated -ip"
setenv CXXFLAGS "-O3 -fPIC -align -Zp8 -axW -unroll -Wno-deprecated -ip"
setenv FFLAGS "-O3 -fPIC -align -Zp8 -axW -unroll -Wno-deprecated -ip"

setenv CPPFLAGS "-I/home/yz30/Intel/FFTW-3.1.2-Lib/include"
setenv LDFLAGS "-L/home/yz30/Intel/FFTW-3.1.2-Lib/lib -L/usr/X11R6/lib64"

./configure --prefix=/scratch/yz30/Intel/Gromacs-3.3.2-FFTW3
--enable-double --with-fft=fftw3 \
--enable-mpi --program-suffix=_mpi_d --disable-nice


Thanks in advance.