[gmx-users] Re: How to ignore atoms during simulations??
cesar.araujo at oulu.fi
Wed Jun 21 15:57:07 CEST 2006
Cesar Araujo wrote:
> 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
>> 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.
Thanks in advance,
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