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

[Tanping Li]

Thanks for the reply. I need to run a lot of
trajectory to get the average. If I increase the box
size, it will consume more computer power. VMD is good
for the single trajectory, but it is hard for every
one.

My box size is already 6.0 nm. But when I calculate
Columb energy between a specific resiue and waters by
Q1*Q2/r, it still can not converge to the  GROMACS
value from g_energy. I use PME. So I am not sure if it
comes from the periodic image of waters.


Best
Tanping


--- Louic Vermeer <science at louic.nl> wrote:

> 
> 
> 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!
> Louic
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