[gmx-users] position restraint

[Anton Feenstra]

herbst at fhi-berlin.mpg.de wrote:

> 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

These are for the water. Position restraints are part of the molecule 
definition, so you should add the line for atom '178' before the inclusion 
of the water (#include spc.itp, or similar) in your .top

> 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.

This is not a crash, it is the periodic box (read the manual... :-0


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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