[gmx-users] dummy atom - regd

ramesh cheerla rameshgromacs at gmail.com
Wed Feb 20 17:53:53 CET 2013

Dear Mark,

Thank you for your reply, I was able to fix the position of  ghost atom by
using   "energygrp_excl " in my mdp file  for energy exclusion between
ghost atom and the remaining  part of the system   and  have removed center
of mass motion by using option comm_mode       = linear .
If  I observe the trajectory the ghost atom is  not moving at all(as I
required)  but remaining system is translating.
Here my question is  though I have used the option comm_mode=linear to
remove the translational motion then  why my system is translating ?  and
moreover I have used  pcoupltype      = anisotropic as I am dealing with
materials it is required, is that because of  that ?

Thank you,


On Mon, Feb 18, 2013 at 4:40 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> 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.
> Mark
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