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> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> 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>> Hi,<br>><br>> I am trying to do some simulation of chloroform system and I need<br>> convert sigma & epsilon to C6 & C12 LJ-parameters.<br>><br>> I use C6=4*epsilon*sigma^6 and C12=4*epsilon*sigma^12 formula.
<br>> This is my result<br>><br>> [ atomtypes ]<br>> ;type mass charge ptype sigma epsilon<br>> CH 12.01100 0.420 A 3.80000e-01 3.26944e-01<br>> CLCL3 35.45300
-0.140 A 3.47000e-01 1.25604e+00<br>><br>> [ atomtypes ]<br>> ;name at.num mass charge ptype c6 c12<br>> CH 6 13.01100 0.000 A 0.39376E-02
0.11856E-06<br>> CL3 17 35.45300 0.000 A 0.87710E-02 0.15300E-06<br>><br>><br>> The sigma and epsilon LJ-parameters is very good to discribe chloroform<br>> box in the molecular topology of user contributions.
<br>> <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>> <<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>> But when I use C6&C12 LJ-parameters I can not get equilibrium and the<br>> moleculars sticked together.<br>><br>cd src/contrib/<br>make sigeps<br>manual chap. 4<br>check combination rules<br><br>
> Thanks in advance.<br>><br>> --<br>> Sincerely yours,<br>> James Jianzhang<br>><br>><br>><br>> ------------------------------------------------------------------------<br>><br>> _______________________________________________
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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.
<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org
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http://www.gromacs.org/search</a> before posting!<br>Please don'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'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
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