I did convert the parameters according to Manual chapter 4.11 and 5.3.3.<br>I used C6=4*epsilon*sigma^6 and C12=4*epsilon*sigma^12 formula.<br>If my conversion is right, then where is wrong?<br><br>I find the same question in the mailing list, but there is no response.
<br><a href="http://www.gromacs.org/pipermail/gmx-users/2004-July/011337.html">http://www.gromacs.org/pipermail/gmx-users/2004-July/011337.html</a><br><br>Why did the same system get totally different simulation result when I changed the L-J expressions?
<br>Thanks.<br><br><div><span class="gmail_quote">On 7/15/07, <b class="gmail_sendername">David van der Spoel</b> &lt;<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>&gt; wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
james zhang wrote:<br>&gt; Hi,<br>&gt;<br>&gt; I am trying to do some simulation of chloroform system and I need<br>&gt; convert sigma &amp; epsilon to C6 &amp; C12 LJ-parameters.<br>&gt;<br>&gt; I use C6=4*epsilon*sigma^6 and C12=4*epsilon*sigma^12 formula.
<br>&gt; This is my result<br>&gt;<br>&gt; [ atomtypes ]<br>&gt; ;type&nbsp;&nbsp;&nbsp;&nbsp;mass&nbsp;&nbsp;&nbsp;&nbsp;charge&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ptype&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;sigma&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;epsilon<br>&gt;&nbsp;&nbsp;CH&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;12.01100&nbsp;&nbsp; 0.420&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; A&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;3.80000e-01&nbsp;&nbsp;3.26944e-01<br>&gt;&nbsp;&nbsp;CLCL3&nbsp;&nbsp; 35.45300
&nbsp;&nbsp;-0.140&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; A&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;3.47000e-01&nbsp;&nbsp;1.25604e+00<br>&gt;<br>&gt; [ atomtypes ]<br>&gt; ;name&nbsp;&nbsp;at.num&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;mass&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;charge&nbsp;&nbsp; ptype&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; c6&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; c12<br>&gt;&nbsp;&nbsp;&nbsp;&nbsp;CH&nbsp;&nbsp;&nbsp;&nbsp;6&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;13.01100&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; A&nbsp;&nbsp; 0.39376E-02
&nbsp;&nbsp; 0.11856E-06<br>&gt;&nbsp;&nbsp; CL3&nbsp;&nbsp; 17&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;35.45300&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; A&nbsp;&nbsp; 0.87710E-02&nbsp;&nbsp;&nbsp;&nbsp;0.15300E-06<br>&gt;<br>&gt;<br>&gt; The sigma and epsilon LJ-parameters is very good to discribe chloroform<br>&gt; box in the molecular topology of user contributions.
<br>&gt; <a href="http://www.gromacs.org/component/option,com_docman/task,cat_view/gid,36/dir,DESC/order,name/limit,5/limitstart,10/">http://www.gromacs.org/component/option,com_docman/task,cat_view/gid,36/dir,DESC/order,name/limit,5/limitstart,10/
</a><br>&gt; &lt;<a href="http://www.gromacs.org/component/option,com_docman/task,cat_view/gid,36/dir,DESC/order,name/limit,5/limitstart,10/">http://www.gromacs.org/component/option,com_docman/task,cat_view/gid,36/dir,DESC/order,name/limit,5/limitstart,10/
</a>&gt;<br>&gt; But when I use C6&amp;C12 LJ-parameters I can not get equilibrium and the<br>&gt; moleculars sticked together.<br>&gt;<br>cd src/contrib/<br>make sigeps<br>manual chap. 4<br>check combination rules<br><br>
&gt; Thanks in advance.<br>&gt;<br>&gt; --<br>&gt; Sincerely yours,<br>&gt; James Jianzhang<br>&gt;<br>&gt;<br>&gt;<br>&gt; ------------------------------------------------------------------------<br>&gt;<br>&gt; _______________________________________________
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<br><br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.
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http://www.gromacs.org/search</a> before posting!<br>Please don&#39;t post (un)subscribe requests to the list. Use the<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org
</a>.<br>Can&#39;t post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><br>-- <br>Sincerely yours,<br>James Jianzhang
<br><br>