how to define different regions in data file(Namely the file with atom coordinates)

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1

Hi, Guys,

These days, i am dealing with a water model with different regions. I can only build up the model with data file where i give the coordinates, bonds and angles. But i can’t define regions in this data file. Although i can define regions in general input file with command: region, but when i run the file, it gave me error: Use of region with undifined lattice. And i tried “units lattice”, “units box”, and without units settings. I still get the same error.

It would be very simple If We can define water parameters(coordinates, bonds, angles,…) in input file directly. But it seems we cannt do that.

Who can give me some suggestions? Thanks in advance.

Bests,

Eric

2

I'm not sure what you mean by defining a region "in a data file".

Regions are volumes in space. Atoms may occupy them, or not. These
atoms may belong to molecules or not.

What are you trying to do with the region command?
Are you just trying to place the water molecules in a specific
location of your simulation box?
In that case you must specify where the water molecules are located in
your data file.

In that case there are several different ways to create a data file
with molecules filling specific locations:

For a simple system try this:
http://sourceforge.net/mailarchive/message.php?msg_id=29621409

For something more complex, try one of the following options:
http://sourceforge.net/mailarchive/message.php?msg_id=29621173
or
http://sourceforge.net/mailarchive/message.php?msg_id=29619703

(PACKMOL generates the coordinates, but not the topology data.
Topotools can generate the topology data.)
http://www.ime.unicamp.br/~martinez/packmol/
http://www.ime.unicamp.br/~martinez/packmol/examples/index.html
http://sites.google.com/site/akohlmey/software/topotools/

Forgive me if I misinterpreted what you are trying to do.
I hope somebody else replies to your question also.

Cheers

Andrew

P.S.
There was a typo in one of the moltemplate examples in one of the threads:
This text:
cells = new UnitCell[3].move(13.8,0,0)
                    [3](0,13.8,0)
                    [3](0,0,13.8)

3

There is no need to define regions in a data file, you are not using the region command correctly. Please read the documentation more carefully and study the examples in the mailing list archives. Axel.