[gmx-users] Re: adding to liquids in the simulation box: one is in the right side of the box and the other in the left side

Vitaly Chaban vvchaban at gmail.com
Mon May 2 15:40:37 CEST 2011

> To do this at first I fill my box using "genbox" with one of the liquids as
> solvent: I used -cs and I did not used -cp.
> and then I used "genbox" again to add the other liquid in it: first liquid
> as a solute and the second one is as solvent. But these two liquids gives
> me
> a solution. I want to prevent mixing of them. what should I do?

1. Create a box.
2. Add the first liquid as usually (using genbox).
3. Equilibrate a system.
4. Enlarge your box in certain direction, i.e. manually change the side
length in GRO file.
5. Add the second liquid (using genbox). To ensure that molecules of the
second type are unable to fit to the voids between the molecules of the
first type, you may somewhat enlarge VDW radius for certain site of molecule
# 2 in the "vdwradii.dat" file.
6. Freeze molecules # 1 and equilibrate the subsystem with molecules # 2.

Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
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