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