Re: Dynamics of an interface Water/Hexane

From: Amy Rice (
Date: Wed Apr 13 2016 - 11:32:09 CDT

Hi Jean-François,
I believe this can be accomplished fairly easily using TclBC or TclForces,
descriptions of which can be found in the user guide and in the
User-Defined Forces tutorial (
Additionally, the Membrane Tutorial (
uses TclForces to keep water out of the bilayer; the tcl script used there
should be fairly straightforward to modify for use in your system.
- Amy

On Wed, Apr 13, 2016 at 7:54 AM, Jean-François Fabre <> wrote:

> Dear all,
> I try to perform a simulation of the interfacial behavior of a
> phospholipid.
> I have constructed a box with a layer of hexane in the middle (147
> molecules considering the density of hexane at 25°C) and two layers of
> water (500+500) on the top and bottom of the box. I inserted a molecule of
> phospholipid at each interface and I performed a NVT calculation at 300K
> with periodic box conditions, wrapping all the atoms and using a Charmm
> forcefield. However, water molecules immediately diffuse in the hexane
> layer. I would like to know how I can avoid this diffusion and maintain the
> interfaces. I tried to add a pressure control (langevin piston) in order to
> be at atmospheric pressure but it doesn't work. How can I force water and
> hexane molecules to remain in their layer (free to move in the x-y
> direction but restrained in the z direction).
> Thank you very much for your answer !
> Regards,
> Jean-François Fabre

Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology

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