[gmx-users] parameter declaration

herbst at fhi-berlin.mpg.de herbst at fhi-berlin.mpg.de
Tue Jun 8 13:32:37 CEST 2004

Hello all,

I have tried to declare bond parameters in my topology-file, e.g.
[ bonds ]
;  ai    aj funct            b0              kb
    1     2     1           1.330000e-01  4.184000e+05

but when I try to generate a .tpr file with grompp I get a warning for
every line of parameter declaration:

WARNING 1 [file "S.top", line 54]:
  No default Bond types for perturbed atoms, using normal values

after a few warnings the program crashes.
What have I done wrong??
And another question:
When I delete all parameters, the simulation works, but the molecule flies
apart, as if no parameters were defined at all. Should the program not use
the parameters out of the .itp file in this case??


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