I did not develop the force field of my molecule by myself. In stead I use the literature force field parameters. I guess not all the force field need the [pairs]. As long as I can get reasonable experimental observables, I can use such force field, right?<br>
<br><div class="gmail_quote">On Tue, Jan 26, 2010 at 6:50 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</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;">
<div class="im"><br>
<br>
----- Original Message -----<br>
From: Yanmei Song <<a href="mailto:ysong30@asu.edu">ysong30@asu.edu</a>><br>
Date: Wednesday, January 27, 2010 10:58<br>
Subject: Re: [gmx-users] Potential Energy<br>
To: <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>, Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
<br>
> Dear Justin:<br>
><br>
> I finally figure out that the problem comes from the Coulomb 1-4 interactions defined by [pairs] part. When I remove this parts, the energy minimization ends with a big negative number. Thanks for your help.<br>
<br>
</div>That's not a solution, that's a random number generator. Whether or not you need such pairs is force-field dependent. Ad hoc changes are ridiculous. Messing with force fields is an expert topic, and parameterizing a new molecule is difficult and risky.<br>
<font color="#888888"><br>
Mark<br>
</font><div><div></div><div class="h5">--<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Yanmei Song<br>Ph.D. Candidate<br>Department of Chemical Engineering<br>Arizona State University<br>