You should get identical plots. I think rule 1 and rule 3 are equivalent.<br><br><div><span class="gmail_quote">On 7/16/07, <b class="gmail_sendername">Janne Hirvi</b> <<a href="mailto:janne.hirvi@joensuu.fi">janne.hirvi@joensuu.fi
</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;">Hello!<br><br>Could you please help me to understand solution as well? I just plotted these
<br>functions so that I combined sigma and epsilon values using rule 3<br><br>sigma(ij)=(sigma(i)*sigma(j))^(1/2)<br>epsilon(ij)=(epsilon(i)*epsilon(j))^(1/2)<br><br>and corresponding C6 (4*epsilon*sigma^6) and C12 (4*epsilon*sigma^12) values
<br>using rule 1<br><br>C6(ij)=(C6(i)*C6(j))^(1/2)<br>C12(ij)=(C12(i)*C12(j))^(1/2)<br><br>and got identical plots. What I have missed?<br><br>Janne<br><br>><br>> My problem has solved. Finally I realized that my calculation is wrong.
<br>> Thank you so much!<br>><br>> On 7/15/07, james zhang <<a href="mailto:james.zhangj@gmail.com">james.zhangj@gmail.com</a>> wrote:<br>> ><br>> > From equation 5.3 page 88, I think rule 1 and 3 are equivalent if you
<br>> > convert the parameters.<br>> > I am sorry. What's the different between rule 1 and 3?<br>> > I think C6/C12 are used in rule 1 and sigma/epsilon are used in rule 3.<br>> > But if you convert sigma/epsilon to C6/C12, these two should be
<br>> equivalent.<br>> > I am confused. Can I convert sigma/epsilon to C6/C12 if I want to use gmx<br>> > force field instead of OPLS ?<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>> wrote:<br>> > ><br>> > > james zhang wrote:<br>> > > > I used rule 3 for ffopls rule 1 for ffgmx.<br>> > > ><br>
> > > please read the manual.these combination rules are not equivalent.<br>> > ><br>> > > there is also combination rule 2, see 5.3.3<br>> > > --<br>> > > David.<br>> > > ________________________________________________________________________
<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</a> <a href="http://folding.bmc.uu.se">
http://folding.bmc.uu.se</a><br>> > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>> > ><br>> > > _______________________________________________<br>> > > gmx-users mailing list
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</a><br></blockquote></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>