7 and 8 have nothing to do with OPLS-AA. As the text tells you, it is the Encad forcefield (http://www.sklogwiki.org/SklogWiki/index.php/ENCAD_%28force_field%29)
So that then leaves you with the OPLS-AA for you to use :-) Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. > -----Original Message----- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of mirc...@sjtu.edu.cn > Sent: Tuesday, 22 February 2011 4:18 PM > To: gmx-users@gromacs.org > Subject: [gmx-users] membrane bilayer simulation by OPLS FF > > Dear All: > > I am using OPLS force field (OPLS FF) to do molecular dynamics > simulations. My system contains DPPC lipid, protein and a small > molecule. I have the following questions: > > 1, where can I get the topology files for the DPPC lipids? > > 2, How to prepare the topology files for the small molecules? I plan > to calculate the charges of each atoms by QM method.After I got the > charges and atom radius, how to prepare the topology files? > > 3, I am using GROMACS 3 and I found there are three all-atom force > fields there: > ---------------------------------------------- > 0: GROMOS96 43a1 force field > 1: GROMOS96 43b1 vacuum force field > 2: GROMOS96 43a2 force field (improved alkane dihedrals) > 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) > 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) > 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) > 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) > 7: Encad all-atom force field, using scaled-down vacuum charges > 8: Encad all-atom force field, using full solvent charges > ------------------------------------------------- > > among them, 6, 7, and 8 are all-atom force fields, right? My question > is are 7 and 8 also OPLS force fields? If so, which one is > recommendated to use in lipid-protein complex systems MD simulations? > What are the differences between 6, 7 and 8. > > Sincerely Yours > > Ruo-Xu Gu > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists