[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
vvchaban at gmail.com
Mon May 2 18:35:15 CEST 2011
On Mon, May 2, 2011 at 11:55 AM, Maria Hamilton
<hamilton.maria39 at gmail.com>wrote:
> 1.Does any liquid have an individual "vdwradii.dat"?
"vdwradii.dat" is one for all atoms. It is in the same directory with
built-in topologies. The atom names in your conf.gro and this "vdwradii.dat"
should coincide, while genbox is operating.
> I found only one "vdwradii.dat" file in GROMACS folder.
> 2.How can I freeze the first liquid?
Use *freeze groups* and *freeze dimensions* keywords. See reference for
parameters in MDP to get exact names of them.
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
> 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
>>> solvent: I used -cs and I did not used -cp.
>>> and then I used "genbox" again to add the other liquid in it: first
>>> as a solute and the second one is as solvent. But these two liquids gives
>>> 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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