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I would like to perform a decane/water(tip4p) interface simulation using GROMACS to analyse the fluctuation of the interface over a long period of time (50ps - 1ns).

Though I have a rough idea on how to perform it, I still am unsure about how to create a initial configuration which looks like the figure give below (A.R. Buuren, Ph.D. Thesis, University of Groningen, 1995). enter image description here

Also once I start my production run I would like to know, how to obtain the height fluctuations of the interface as a function of time.

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A simple solution to begin with would be to create two systems: one with decane in a box of width 1.295nm and another one with water in a box of width 2nm (depth and height should be as in the picture you included with your question).

Once you have the two systems, run them independently for a sufficiently long time so that they equilibrate. Then take two snapshots (sets of positions and velocities) of the decane box that are uncorrelated and one snapshot of the water box. Translate the positions of the water and one of the decane boxes so that they form the configuration you want. You can do this, for example, with VMD or with MDTraj.

Finally, create the target system having all the molecules but with the conformations (and velocities) taken from the translated boxes that you obtained in the previous step. Equilibrate again, and run.

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