I used rule 3 for ffopls rule 1 for ffgmx.<br><br>sigma/epsilon<br><br>[ defaults ]<br>; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br>1 3 yes 0.5 0.5<br><br>C6/C12<br><br>[ defaults ]<br>
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br> 1 1 no 1.0 1.0<br><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>> 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>how about the defaults section (chapter 5)
<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<br>> changed the L-J expressions?<br>> Thanks.<br>><br>> On 7/15/07, *David van der Spoel* <<a href="mailto:spoel@xray.bmc.uu.se">
spoel@xray.bmc.uu.se</a><br>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>> wrote:<br>><br>> 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<br>> 0.11856E-06<br>> > CL3 17 35.45300 0.000 A<br>> 0.87710E-02 0.15300E-06<br>> ><br>> ><br>> > The sigma and epsilon LJ-parameters is very good to discribe
<br>> chloroform<br>> > box in the molecular topology of user contributions.<br>> ><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>> ><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>> ------------------------------------------------------------------------
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<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">
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> James Jianzhang<br>><br>><br>> ------------------------------------------------------------------------<br>><br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
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</div><br><br clear="all"><br>-- <br>Sincerely yours,<br>James Jianzhang<br>Department of Mechanical and Chemical Engineering <br>North Carolina Agricultural and Technical State University <br>1601 East Market Street <br>
Greensboro, NC 27411 <br><a href="mailto:jzhang@ncat.edu">jzhang@ncat.edu</a> or <a href="mailto:james.zhangj@gmail.com">james.zhangj@gmail.com</a><br><a href="http://www.ncat.edu/~jzhang">http://www.ncat.edu/~jzhang</a>