Re: Dynamics of an interface Water/Hexane

From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Fri Apr 15 2016 - 07:39:43 CDT

Sounds like you want to apply restraints with regards to absolute positions of atoms. Use TclBC for that. The script will be extremely simple. Reply here if you have troubles following tclbc tutorials (google them up).

> On Apr 13, 2016, at 07:54, 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
>
>

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