[gmx-users] dummy atom - regd

ramesh cheerla rameshgromacs at gmail.com
Wed Feb 20 17:33:47 CET 2013

Dear Bogdan,

  Thank you for reply.


On Mon, Feb 18, 2013 at 5:31 PM, Bogdan Costescu <bcostescu at gmail.com>wrote:

> On Mon, Feb 18, 2013 at 12:10 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> > b) a particle needs to be at that immobile reference point - you can
> > measure a distance to a point whether or not there is something there.
> I'm not sure that it's the same use-case... I recently talked to
> someone trying to define such a fixed particle to be used as a pull
> group.  This pull group could then be set as reference in the middle
> of the PBC box, such that the pull distances are smaller than half the
> box size. The fact that the particle is really fixed when the PBC box
> is allowed to change dimensions is not a big problem, if needed the
> size of the box for each trajectory frame can then be used to correct
> distances. I don't know what was the outcome, but I'm curious to see
> such a setup.
> Cheers,
> Bogdan
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