[gmx-users] dummy atom - regd

Mark Abraham mark.j.abraham at gmail.com
Mon Feb 18 12:10:56 CET 2013

On Mon, Feb 18, 2013 at 4:27 AM, ramesh cheerla <rameshgromacs at gmail.com>wrote:

> Dear Mark,
> Thank you  very much for your reply,
> As I am performing meta-dynamics simulations in GROMACS  with PLUMED patch
> grid, I want the distance between the  immobile  atom and the mobile atom
> to be my collective variable. If I take  distance between two mobile  atoms
> as my  collective variable both atoms  are moving  together or  moving in
> opposite directions. I want to decouple  the contribution from the mobile
> reference to my free energy profile.
> Is it possible to have immobile reference like this(as mentioned in
> previous mail) ?

I still don't understand why
a) immobility of the reference point makes it possible to do something
useful that can't be done otherwise, and
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.
If this is a real need case for PLUMED, then perhaps exploring the point
with its authors will be a useful step.


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