<div id="RTEContent">Hi,<br> <br> take a look at the sw.itp file in share/top in your gromacs installation directory. it is an example for water. You could modify it for your use. there are useful comments in it too.<br> <br> o.<br><br><b><i>Yinghong <xieyh@hkusua.hku.hk></i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> <meta http-equiv="Content-Type" content="text/html; charset=gb2312"> <meta content="MSHTML 6.00.2900.2769" name="GENERATOR"> <div>Dear Gmx'ers:</div> <div> </div> <div>As mentioned in the publication about shell water model, a shell particle is connected to a dummy atom by a spring-like connection with the following relationship:</div> <div> </div> <div>1. K=sqr(qS)/(4*PHI*Epsilon*alpha), </div> <div>2. rsd=(4*PHI*Epsilon*alpha)*E / qS; (rsd is the distance between shell and dummy particles at any moment, and E is refered to electrical field strength).</div>
<div> </div> <div>Anyone can tell me where is the definition of two equations above, especially in the case of<strong> "isotropic polarization",</strong> in GMX source code.</div> <div>Because in my simulation, what I want to polarized is not a water molecule. So I need a definite instruction, any suggestion?</div> <div> </div> <div>Secondly, how can I read the calculated value of spring constant K by GMX after I defined "alpha" and "qS"? Can "debug" realize it? If yes, how? Although I have used GMX for a long time, but that is the first time for me to encounter such a problem.</div> <div> </div> <div>Waiting for your response, any instruction will be greatly appreciated.</div> <div> </div> <div> </div> <div>Xie Yinghong</div> <div>Hong Kong Univ.</div>_______________________________________________<br>gmx-users mailing list<br>gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please don't
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