[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:
>> 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
>> those atoms has zero mass and the program stops after certain numbers
>>> Well you've still got bonded and LJ interactions acting to create
>>> on particles with zero mass so it is no great surprise that things
>>> breaking. Probably what you want to do is go back to square one and
>>> topologies that don't have these atoms, but you haven't described
>>> chemistry, so we can't help you there.
> Well, my idea is to "delete" atoms and then "undelete" them without
> coordinates file. I guess that it could be done just touching topology
> Is it correct??? The results I'm looking for is to turn invisible some
> Any suggestion???
> Thanks in advance,
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Pradip K. Biswas, PhD.
Research Associate, Department of Chemistry;
Cleveland State University, Ohio-44115
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