Hi, I am trying to build itp file for polymer simulations using OPLS-AA and had two questions I could not find a clear answer from the forum or the manual.
1. Is the order of bond types listed in a row of the [dihedral] section important, i.e. if I replace ijkl by lkji, will this make any differences. Since type 3 is the RB dihedral, I see that the form sum_n C_n (cos(psi))^n is unchanged with a transformation psi=-psi (or dihedral angle, phi=-phi) but not sure. Note that I explicitly list the dihedral parameters for some of the rows in the itp file, when the default parameters do not exist in ffbonded.itp (in somewhat ad-hoc way for the moment by finding the closest existing set. comments?). 2. Should I have 1-4 exclusions listed in [ pairs ] section for OPLS-AA? I find conflicting statements when I searched on this. For example, methanol.itp file in the OPLS-AA force-field directory lists the exclusions. Thanks! P -- View this message in context: http://gromacs.5086.x6.nabble.com/Atom-ordering-for-RB-dihedrals-in-OPLS-AA-tp5011021.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
