<br><br><div class="gmail_quote">On Tue, Nov 10, 2009 at 4:32 AM, Marcovitz Amir <span dir="ltr"><<a href="mailto:amarcovitz@gmail.com">amarcovitz@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Amit,<br>
<br>
Unfortunately, i don't have an answer to your question as i am a very<br>
new GROMACS user myself..<br>
Actually i might need your help.<br></blockquote><div> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I need to model two charged plates with opposite signs which are<br>
solvated in an electrolyte solution. </blockquote><div><br>You might try to start with a boundary condition on the potential say something like constant potential on the plates. And then you can always find the electrostatic Green's function that solves the poisson's equation. From there you could derive an expression for the potential in the box if the charge density were provided. This part is discussed in Classic Electrodynamics book by Jackson. Have a look at it if you need reference.<br>
<br>You can use the above green's function for finding potential everywhere in box depending on the location of ions in the solution. The force due to this can then be implemented in MD. I am not very sure about the implementation though.<br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">When I was desperately browsing for<br>
keywords such as: Gromacs plates, walls, etc., trying to find the<br>
slightest clue of how to approach this issue in gromacs i saw your<br>
posting from the October 19th.<br>
<br>
I will most appreciate if you can give me some hint or tip of how to<br>
approach this problem or what is the suitable chapter in the manual to<br>
search for it.<br></blockquote><div><br>I am not sure about any discussion on the specific type of things you are talking about. Wall function for MD simulation is disscussed in chapter 7. You will only find what options can be used. I think a tabulated function can also be used.<br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Sorry i couldn't help you with your question, hopefully you already<br>
figured it out,<br></blockquote><div><br><br>I think it beneficial for both of us to keep these discussion in the forum for our and other's benefit .<br><br>Amit <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Regards,<br>
<font color="#888888">Amir Marcovitz,<br>
Weizmann Inst. of Science , Rehovot, Israel<br>
</font></blockquote></div><br>