That really depends on where the function that you are using comes from and what forcefield you are using (because each forcefield can treat them differently). If it is the one for alkane chains mentioned in the manual to be used with the GROMOS FFs, then as it states in the manual you have to remove pairs. If it comes from the OPLS FFs, then you need to leave the pairs in.
Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 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 Marcelo Vanean > Sent: Tuesday, 14 May 2013 8:24 AM > To: gmx-users@gromacs.org > Subject: [gmx-users] Fwd: Rycaert-Bellemans function > > Hello to all. I am simulating long-chain alcohols. For the dihedrals, I > used Rycaert-Bellemans function. In this case I should delete the pairs > from topology? > -- > 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
