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

Pradip Kumar Biswas p.biswas at csuohio.edu
Wed Jun 21 16:18:29 CEST 2006

I was wondering whether one can have atom types with zero charge, zero 
vdw (C6=0, C12=0; Or sigma=0; epsilon=0), but with mass. Won't they be 
invisible in the energy/force calculations (if they are not connected 
by any bonded interaction)?


On Jun 21, 2006, at 9:57 AM, Cesar Araujo wrote:

> 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.-
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Pradip K. Biswas, PhD.
Research Associate, Department of Chemistry;
Cleveland State University, Ohio-44115
Phone: 1-216-875-9723
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