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Re: [lammps-users] LAMMPS library: Gather specific atoms and insert small molecules
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Re: [lammps-users] LAMMPS library: Gather specific atoms and insert small molecules


From: Stephan Grein <stephan.grein@...5733...>
Date: Fri, 15 Sep 2017 19:48:19 +0200

> 
>     3) create_atoms can create/distribute
>     random atoms. I need however to create
>     small molecules and distribute them
>     randomly. The small molecule structure
>     is known a-priori, however I need to
>     insert let's say 10 randomly in my
>     simulation box.
> 
> 
> with a recent enough version of LAMMPS, ​create_atoms can also create
> molecules that have been previously defined with the molecule command
> and read from a suitable file.

Follow up on this:
If I would add a new ion type to my system,
I would have to specify obviously all the
interactions with the other types in my system.
Correct? So would it be better to prepare the
ion in a let's say dummy PDB file and convert
it to a LAMMPS input data with e.g. topotools
and then use read_data?

Best regards,
Stephan


> 
> ​axel​
> 
>  
> 
> 
>     Thanks in advance.
> 
>     Best regards,
>     Stephan
> 
> 
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> 
> 
> -- 
> Dr. Axel Kohlmeyer  akohlmey@...24... <mailto:akohlmey@...24...>
>  http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.

-- 
Stephan Grein
Department of Mathematics
Temple University
1805 N Broad Street, Room 513
Philadelphia, PA 19122-6094, USA
https://math.temple.edu/~queisser/
phone: +1 (215) 434-5843

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