Re: Constraining and imparting motion to a geometry

From: Jérôme Hénin (
Date: Mon Sep 04 2017 - 07:42:47 CDT

Hello Abhay,

The position constraints are absolute, they will conflict with a moving
restraint such as SMD. To keep the conformation fixed, you probably want to
restrain an *RMSD* collective variable. If you need to restrain the
*orientation* as well, have a look at the collective variable component of
the same name.


On 1 September 2017 at 21:47, Abhaysinh Gaikwad <>

> Hello all,
> My system has two objects/geometries, one of silicon and one of gold. The
> gold substrate is fixed at the bottom using fixed atom constraints. The
> substrate with silicon is on the top and needs to be moved to the gold
> atoms at a given velocity. However, the silicon atoms need to maintain
> their shape configuration during downward movement. I am constraining the
> silicon atoms to maintain their shape configuration by following script.
> constraints on
> consRef
> consKFile
> consKCol
> selectConstraints on
> selectConstrX on
> selectConstrY on
> selectConstrZ off
> But, before even SMD starts the silicon geometry gets break and it
> expands. For SMD I am using following script
> SMD on
> SMDFile
> SMDk
> SMDVel
> SMDDir
> SMDOutputFreq
> Can anyone suggest how we can maintain the silicon shape/geometry constant
> and pull it down to the gold substrate?
> Thank you,
> Abhay

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