I am trying to complete the lysozyme in water tutorial in gromacs 4.6.1 and
i am getting this error in the energy minimization step
I was able to complete the entire tutorial on another computer ( my
personal laptop) . ( I was getting the same error while doing energy
minimization on another system (polymer in water) which forced me to check
gromacs correcctness by doing the lysozyme tutorial)
The following is the verbose output to my terminal :
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Step= 0, Dmax= 1.0e-02 nm, Epot= -nan Fmax= 1.50489e+13, atom=
14918
-------------------------------------------------------
Program mdrun, VERSION 4.6.1
Source code file: /home/vishal/Downloads/gromacs-4.6.1/src/mdlib/pme.c,
line: 827
Fatal error:
3483 particles communicated to PME node 2 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension x.
This usually means that your system is not well equilibrated.
Following is the entry from "em.log" file
Linking all bonded interactions to atoms
There are 8522 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME
The initial number of communication pulses is: X 1
The initial domain decomposition cell size is: X 1.83 nm
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 1.000 nm
two-body bonded interactions (-rdd) 1.000 nm
multi-body bonded interactions (-rdd) 1.000 nm
Making 1D domain decomposition grid 4 x 1 x 1, home cell index 0 0 0
Initiating Steepest Descents
Charge group distribution at step 0: 3184 3300 3308 3255
Grid: 5 x 11 x 11 cells
Started Steepest Descents on node 0 Mon May 20 11:36:21 2013
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Step Time Lambda
0 0.00000 0.00000
DD step 0 load imb.: force 8.8%
-------------------------------------------------------
Program mdrun, VERSION 4.6.1
Source code file: /home/vishal/Downloads/gromacs-4.6.1/src/mdlib/pme.c,
line: 827
Fatal error:
3483 particles communicated to PME node 2 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension x.
This usually means that your system is not well equilibrated.
The following is the hardware information of the pc on which error is
showing ttaken from "em.log" file
Gromacs version: VERSION 4.6.1
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled
GPU support: disabled
invsqrt routine: gmx_software_invsqrt(x)
CPU acceleration: AVX_256
FFT library: fftw-3.3.3-sse2
Large file support: enabled
RDTSCP usage: enabled
Built on: Fri May 10 13:45:48 IST 2013
Built by: vishal@aditya-HCL-Desktop [CMAKE]
Build OS/arch: Linux 3.0.0-19-generic x86_64
Build CPU vendor: GenuineIntel
Build CPU brand: Intel(R) Core(TM) i5-2400 CPU @ 3.10GHz
Build CPU family: 6 Model: 42 Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
nonstop_tsc pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2
ssse3 tdt x2apic
C compiler: /usr/bin/gcc GNU gcc (Ubuntu/Linaro 4.6.1-9ubuntu3)
4.6.1
C compiler flags: -mavx -Wextra -Wno-missing-field-initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer
-funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG
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