[MMTK] Creating a Liquid-Liquid Interface

Konrad Hinsen research at khinsen.fastmail.net
Fri Jul 16 13:32:43 UTC 2010


On 15.07.2010, at 17:51, Victor Akujobi wrote:
> Hello Everyone, I would like to ask for a  favour. I'm fairly new to MMTK so I apologize if this is a dumb question.
> 
> Let's say I want to create 2 solvent boxes (one organic and one aqeous), and then add them to a universe to form a liquid-liquid interface. I have pdbs of both comopunds, what would be the best way to go about this.

For creating the two solvent boxes: look at the example script for adding solvate:

	http://dirac.cnrs-orleans.fr/MMTK/using-mmtk/mmtk-example-scripts/molecular-dynamics/solvating-a-protein-1/

Replace the protein by a solvent molecule, and you have a script that sets up and equilibrates a solvent box. You may want to change the shape of the box in view of the later combination of the two boxes.

One problem: having PDB files of each molecule is not sufficient. You need to have force field parameters as well. If you can't find them, you have to compute/fit them yourself using some suitable reference data, usually from quantum chemistry. Depending on your molecules, that might be a research project in itself. Once you have your parameters, here is how to get them into MMTK:

	http://dirac.cnrs-orleans.fr/Manuals/MMTK/MMTK_7.html

Once you have your two boxes, you need to decide how you want to combine them. Actually doing so is a rather simple exercise with MMTK: you read in the two solvent boxes, create a third universe, and the copy each object from each box into the new universe, applying some geometrical transformation to the coordinates (at least a translation).

I hope this helps as a first guideline.

Konrad.
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research at khinsen dot fastmail dot net
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