From: Amy Rice (arice3_at_hawk.iit.edu)
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 (
http://www.ks.uiuc.edu/Training/Tutorials/science/forces/forces-tutorial.pdf).
Additionally, the Membrane Tutorial (
http://www.ks.uiuc.edu/Training/Tutorials/science/membrane/mem-tutorial.pdf)
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 <
JeanFrancois.Fabre_at_ensiacet.fr> 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
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:20 CST