[gmx-users] How to get the coordinate of periodic image

Louic Vermeer science at louic.nl
Tue Sep 13 16:44:22 CEST 2005

Tanping Li wrote:
> Hellow, evergyone,
> I posted the question last week, but didn't get the
> response. I reaaly have no idea, so I post it again.
> I am analysing the interaction between a specific
> residue in protein and the close waters. Because
> Columb is long-term interaction, I need to consider
> some periodic images of waters. How to get the
> coordinates of those waters? Thank you for your help.

Why don't you make the box larger? That looks more reasonable to me. (IMHO)

The periodic waters are the same waters that are on the other side of 
the box (which is the definition of PBC). The visualization program VMD 
can display periodic images, and can also save their coordinates. There 
are some other ways, but this is the easiest.

> Best
> Tanping

Good luck!

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