Justin,<br><br> The sodium ion I am talking about is part of the docusate sodium salt (AOT). If I want to solvate 100 AOT molecules with water molecules, how do I make sodium ions part of the system? I am not just adding sodium ions to balance the charge of the system. The sodium ions are part of the AOT molecules, so I need 100 sodium ions in the system. Do I just add one sodium ion in the parameter file containing the rest of the 65 atoms of AOT, then specify #include "ions.itp" in the fopology?<br>
I appreciate your answers. <br><br>(Aside: Can you help with replying emails via this forum. I use gmail and when I click the reply tab, it includes all the mails for that issue, and there is no "subject" entry. So I always have to copy and paste the mail before replying. I appreciate your help).<br>
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Lum Nforbi wrote:<br>
> Hi All,<br>
><br>
> I would like to include sodium ions into a water/AOT (sodium<br>
> di-2-ethylhexylsulfoccinate) cubic box. Can someone tell me how to do<br>
> this and how to include parameters for the sodium ion in the parameter file?<br>
> I appreciate your answers.<br>
<br>
Shouldn't this be as simple as using genion and then:<br>
<br>
#include "ions.itp"<br>
<br>
in the topology? Or is there some other problem you're having?<br>
<br>
-Justin<br>
<br>
><br>
> Lum<br>
><br>
<br>
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