[gmx-users] Multiple Bonds

[David L. Bostick]

Hello:

I have a system which ran using Gromacs-2.0.  Recently, I have installed
gmx-3.0, and made appropriate changes to the .mdp file so that I grompp
would write out a .tpr file with no complaints.  However, when I submit the
job using mdrun, the program skips out.  In the beginning of the .log file
there
appears:

box (3x3):
   box[    0]={ 7.47452e+00,  0.00000e+00,  0.00000e+00}
   box[    1]={ 0.00000e+00,  8.38454e+00,  0.00000e+00}
   box[    2]={ 0.00000e+00,  0.00000e+00,  7.56623e+00}
ekin (3x3):
   ekin[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   ekin[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   ekin[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
pres (3x3):
   pres[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   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.  Is there any other reason I might recieve this
message in the mdrun .log file?

Thank you in advance to whomever responds,
David

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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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