[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

Maria Hamilton hamilton.maria39 at gmail.com
Mon May 2 17:55:47 CEST 2011

1.Does any liquid have an individual "vdwradii.dat"?
I found only one "vdwradii.dat" file in GROMACS folder.
2.How can I freeze the first liquid?



On Mon, May 2, 2011 at 6:10 PM, Vitaly Chaban <vvchaban at gmail.com> wrote:

> 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 preovent 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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