From: Jérôme Hénin (
Date: Sat Jul 21 2018 - 06:06:53 CDT

Dear Abhijit,

Do you want to constrain (or restrain) each atom individually, or the
center of mass of groups of atoms? In the second case, your most flexible
choice is Colvars (,
using the *distance* and *distanceXY* coordinates.


On Fri, 20 Jul 2018 at 08:18, Abhijit Gogoi <>

> Dear All,
> I want to constrain 2 parts of my simulation system. For
> one part I want to apply constrain in all (X,Y,Z) directions and for the
> other part I want to apply constrain only is XY plane. Is it possible with
> "constraints" option of NAMD.
> I have tried "constraints" option for one part for constraining all the
> directions and for constraining the other part in XY plane I have used
> "SMD". However with SMD only center of mass will be constrained, but I want
> to constrain each atom of that part.
> Please suggest something.
> sincerely
> Abhijit Gogoi

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