You should get identical plots. I think rule 1 and rule 3 are equivalent.
On 7/16/07, Janne Hirvi <[EMAIL PROTECTED]> wrote:
Hello! Could you please help me to understand solution as well? I just plotted these functions so that I combined sigma and epsilon values using rule 3 sigma(ij)=(sigma(i)*sigma(j))^(1/2) epsilon(ij)=(epsilon(i)*epsilon(j))^(1/2) and corresponding C6 (4*epsilon*sigma^6) and C12 (4*epsilon*sigma^12) values using rule 1 C6(ij)=(C6(i)*C6(j))^(1/2) C12(ij)=(C12(i)*C12(j))^(1/2) and got identical plots. What I have missed? Janne > > My problem has solved. Finally I realized that my calculation is wrong. > Thank you so much! > > On 7/15/07, james zhang <[EMAIL PROTECTED]> wrote: > > > > From equation 5.3 page 88, I think rule 1 and 3 are equivalent if you > > convert the parameters. > > I am sorry. What's the different between rule 1 and 3? > > I think C6/C12 are used in rule 1 and sigma/epsilon are used in rule 3. > > But if you convert sigma/epsilon to C6/C12, these two should be > equivalent. > > I am confused. Can I convert sigma/epsilon to C6/C12 if I want to use gmx > > force field instead of OPLS ? > > Thanks. > > > > On 7/15/07, David van der Spoel < [EMAIL PROTECTED]> wrote: > > > > > > james zhang wrote: > > > > I used rule 3 for ffopls rule 1 for ffgmx. > > > > > > > please read the manual.these combination rules are not equivalent. > > > > > > there is also combination rule 2, see 5.3.3 > > > -- > > > David. > > > ________________________________________________________________________ > > > > > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > > > Dept. of Cell and Molecular Biology, Uppsala University. > > > Husargatan 3, Box 596, 75124 Uppsala, Sweden > > > phone: 46 18 471 4205 fax: 46 18 511 755 > > > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > > > > > _______________________________________________ > > > gmx-users mailing list gmx-users@gromacs.org > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at http://www.gromacs.org/search before > > > posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to [EMAIL PROTECTED] > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- Sincerely yours, James Jianzhang Department of Mechanical and Chemical Engineering North Carolina Agricultural and Technical State University 1601 East Market Street Greensboro, NC 27411 [EMAIL PROTECTED] or [EMAIL PROTECTED] http://www.ncat.edu/~jzhang
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