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

[leafyoung81-group at yahoo.com]

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?

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.-


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</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>


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