[gmx-users] dummy atom - regd

ramesh cheerla rameshgromacs at gmail.com
Mon Feb 18 04:27:12 CET 2013

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) ?

Thank you,


On Mon, Feb 18, 2013 at 12:09 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> On Sun, Feb 17, 2013 at 7:00 PM, ramesh cheerla <rameshgromacs at gmail.com
> >wrote:
> > a immobile
> > reference in my system to measure distance between mobile and immobile
> > one  along a particular axis ?
> >
> If the point is immobile and non-interacting, why do you need a dummy
> particle there?
> Mark
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