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

[Pradip Kumar Biswas]

On Jun 21, 2006, at 11:08 AM, <leafyoung81-group at yahoo.com> wrote:

> Totally delete it from the itp shall be alright. Having a mass makes 
> the atom visible to COM removal. What's the intention to make it 
> invisible?

Like tackling the situation of doing QMMM with Gromos united atom ff.

pb.

>
> Yang Ye
>
> ----- Original Message ----
> From: Pradip Kumar Biswas <p.biswas at csuohio.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Wednesday, June 21, 2006 10:18:29 PM
> Subject: Re: [gmx-users] Re: How to ignore atoms during simulations??
>
> 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)?
>
> pb.
>
> 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
> http://comppsi.csuohio.edu/groups/people/biswas.html
> 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)?
>
>
> pb.
>
>
> On Jun 21, 2006, at 9:57 AM, Cesar Araujo wrote:
>
>
> <excerpt>Cesar Araujo wrote:
>
> <excerpt>Hi,
>
>
> Could anybody tell me how to modify an ITP file to ignore certain
> atoms (as
>
> </excerpt>if
>
> <excerpt>they were not there) during simulations? I've changed charge
> and masses to
>
> </excerpt>0.0
>
> <excerpt>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.
>
> </excerpt>
>
> <excerpt><excerpt>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.
>
> </excerpt></excerpt>
>
> 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.-
>
>
> _______________________________________________
>
> gmx-users mailing list    gmx-users at gromacs.org
>
> http://www.gromacs.org/mailman/listinfo/gmx-users
>
> Please don't post (un)subscribe requests to the list. Use the
>
> www interface or send it to gmx-users-request at gromacs.org.
>
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
> </excerpt>--
>
> Pradip K. Biswas, PhD.
>
> Research Associate, Department of Chemistry;
>
> Cleveland State University, Ohio-44115
>
> Phone: 1-216-875-9723<italic>
>
> http://comppsi.csuohio.edu/groups/people/biswas.html </italic>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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>
> _______________________________________________
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--
Pradip K. Biswas, PhD.
Research Associate, Department of Chemistry;
Cleveland State University, Ohio-44115
Phone: 1-216-875-9723
http://comppsi.csuohio.edu/groups/people/biswas.html
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