[gmx-users] Multiple Bonds

David L. Bostick dbostick at physics.unc.edu
Wed Oct 10 19:27:22 CEST 2001

Dear users,

I recently posted an email asking about a problem with paralellel
gromacs-3.0.  A system that I had previously ran on gromacs-2.0 in parallel
on an IBM SP gives complaints in gromacs 3.0.  grompp gives no errors upon
building the topology, but mdrun skips out immediately with the following
message in the .log file:

   pres[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   pres[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
vir (3x3):
   vir[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   vir[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   vir[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
There are 0 atoms for free energy perturbation
Max number of bonds per atom is 4
Fatal error: More than 10 bonds per atom (atom 3306)

I have checked atom 3306 and those immediately in front and behind in the
array, but all bonds seem to be correct.  I checked the output
grompp.log using grompp -debug.  I also fingered through the output
produced by gmxdumping the .tpr file.  All of these files seemed to posess
the correct connectivity (at most, 4 bonds per atom).

I tried the same grompp command for one processor and also for 5
processors to run a minimization job on the same machine.  The job then
finished successfully for both .  Does anyone know any reason that the 10
processor job gives this error whereas the others do not?

 Thank you in advance,

David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165 
Program in Molecular and Cellular Biophysics 
UNC-Chapel Hill					
CB #3255 Phillips Hall				dbostick at physics.unc.edu	
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick	

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