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

Cesar Araujo cesar.araujo at oulu.fi
Wed Jun 21 15:57:07 CEST 2006

Cesar Araujo wrote:
> Hi,
> Could anybody tell me how to modify an ITP file to ignore certain atoms (as
> they were not there) during simulations? I've changed charge and masses to
> 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.


Well, my idea is to "delete" atoms and then "undelete" them without touching
coordinates file. I guess that it could be done just touching topology files.
Is it correct??? The results I'm looking for is to turn invisible some atoms.

Any suggestion???

Thanks in advance,


More information about the gromacs.org_gmx-users mailing list