Re: XY constraints with center of mass movements

From: Aron Broom (
Date: Mon Dec 09 2013 - 12:00:33 CST

what colvar did you use to try the initial Z-axis pull?

On Mon, Dec 9, 2013 at 12:29 PM, Peterson J <> wrote:

> Hi all,
> I am doing an SMD simulation where I am pulling a molecule in Z-axis for
> about 40 Ang (through the lipid bilayer from slightly above the head
> groups). During my simulation I have seen the molcule moving too much in X
> and Y direction too (it even fluctuating between the PBC copies). I have
> tried then constraining it using selective constraints using selectConstrX
> and selectConstrY options in harmonic constraints option. In this case the
> molecule went straight down in Z-axis not moving (rotating) in its axis.
> I would like to pull the molecule in Z direction with its center of mass
> movements. I need your help.
> Peter

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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