[gmx-users] Help with water decane interface

Justin A. Lemkul jalemkul at vt.edu
Sun Mar 30 15:46:41 CEST 2008

Quoting fabracht sdf <fabracht at gmail.com>:

> *Dear Gromacs users. I ve been trying to run a MSD for a G coupled receptor
> and encountered some problems during my run.
> I have encountered a methodology that deals with this type of transmembrane
> proteins, and apparently I need to assemble my box with a "tri" layer,
> water/decane/water. I found an article entitled "A molecular Dynamics Study
> of the Decane/water interface", where the author studies several aspects in
> the usage of such boxes.
> I need help on how to put together all these water molecules and decane
> molecules in the same box.
> I thought about simply creating theses boxes in separate using gromacs, and
> then simply copying and pasting the coordenates of the molecules into the
> same topology file. Apparently I was too naive to think that this simplistic
> approach would actually work.

Right, well coordinate files and topology files are different, but you've
probably already figured that out.  Have a look at reference material regarding
membrane simulations, especially here:


Basically, you will need to do a few things:

1. Generate coordinates/topology for your protein (pdb2gmx)
2. Coordinates/topology for the decane slab (create a slab from one molecule,
using genconf and then equilibrate)
3. Overlay the coordinate files and delete overlapping decane molecules. 
Several methods for doing this are discussed in the list archive.  Have a
thorough look through past posts.
4. Solvate using genbox.

Having a look through some other basic GROMACS tutorials would probably be a
good idea, especially when it comes to how to include the topologies for all
these components (Chapter 5 in the manual).


> Thank you in advance * <gmx-users at gromacs.org>


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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