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?
Thanks Regards Maria On Mon, May 2, 2011 at 6:10 PM, Vitaly Chaban <vvcha...@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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