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

[Cesar Araujo]

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


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,

César.-