On Mon, May 2, 2011 at 11:55 AM, Maria Hamilton <[email protected]>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 <[email protected]> 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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