[gmx-users] How to ignore atoms during simulations??

[Mark Abraham]

Cesar Araujo wrote:
> Hi,
> 
> Could anybody tell me how to modify an ITP file to ignore certain atoms (as if
> they were not there) during simulations? I've changed charge and masses to 0.0
> but I've got a lot of warnings during grompp preprocessing telling me that
> those atoms has zero mass and the program stops after certain numbers of
> warnings.

Well you've still got bonded and LJ interactions acting to create forces 
on particles with zero mass so it is no great surprise that things are 
breaking. Probably what you want to do is go back to square one and make 
topologies that don't have these atoms, but you haven't described your 
chemistry, so we can't help you there.

Mark