<br><br><div class="gmail_quote">On Mon, May 2, 2011 at 11:55 AM, Maria Hamilton <span dir="ltr"><<a href="mailto:hamilton.maria39@gmail.com">hamilton.maria39@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
1.Does any liquid have an individual "vdwradii.dat"?<br></blockquote><div><br></div><div>"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.</div>
<div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">I found only one "vdwradii.dat" file in GROMACS folder.<br>2.How can I freeze the first liquid?<br>
</blockquote><div><br></div><div><br></div><div>Use *freeze groups* and *freeze dimensions* keywords. See reference for parameters in MDP to get exact names of them.</div><div> </div><br>-- <br>Dr. Vitaly V. Chaban, Department of Chemistry<br>
University of Rochester, Rochester, New York 14627-0216<div><br></div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="gmail_quote">
On Mon, May 2, 2011 at 6:10 PM, Vitaly Chaban <span dir="ltr"><<a href="mailto:vvchaban@gmail.com" target="_blank">vvchaban@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
<div class="gmail_quote"><div><div></div><div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">To do this at first I fill my box using "genbox" with one of the liquids as<br>
solvent: I used -cs and I did not used -cp.<br>
and then I used "genbox" again to add the other liquid in it: first liquid<br>
as a solute and the second one is as solvent. But these two liquids gives me<br>
a solution. I want to preovent mixing of them. what should I do?<br></blockquote><div><br></div><div><br></div></div></div><div>1. Create a box.</div><div>2. Add the first liquid as usually (using genbox).</div><div>3. Equilibrate a system.</div>
<div>4. Enlarge your box in certain direction, i.e. manually change the side length in GRO file.</div><div>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.</div>
<div>6. Freeze molecules # 1 and equilibrate the subsystem with molecules # 2.</div><div><br></div><div> </div></div>-- <br>Dr. Vitaly V. Chaban, Department of Chemistry<br>University of Rochester, Rochester, New York 14627-0216<br>
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