[gmx-users] position restraint

herbst at fhi-berlin.mpg.de herbst at fhi-berlin.mpg.de
Mon Jan 3 15:07:25 CET 2005

Hello all,

I am trying to use the position restaint function for two atoms im my
protein and have added the following lines to my topology file:

[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
 178    1       1000       1000       1000

When I try to create a tpr file with grompp, I get the following error

Fatal error: [ file "smhelix.top", line 1189 ]:
             Atom index (178) in position_restraints out of bounds (1-3)

When I try to run the simulation without pos restraint, the simulation
crashes after a few timesteps. In ngmx the molecule seems to fly out of
the box from one timestep to the next.
Any idea what I should do to get the simulation running?


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