On Sun, Nov 13, 2011 at 10:26 AM, XUEMING TANG <yujan2...@gmail.com> wrote: > Hi there > > I am trying to build up a topology file for a tetra nitrogen molecule using > Gromos UA and OPLS UA force field. Following are the molecules. > > 1. for C > | > A. C-C-C-C-C-C-C-N-C and > | > C > > C > | > B. C-C-C-C-C-C-C-N-C-C-C-C-COOH > | > C > > I have several questions: > > For A, the first molecule, should I use improper dihedral for the N-(CH3)3 > or proper dihedral for C-C-N-C with multi 3 for the head group? Is there any > differences when using different force field (GROMOS and OPLS-UA)? > For B, the second molecule, should I use improper dihedral for the N-(CH3)3 > or proer dihedral for C-C-N-C with multi 2? Is there any differences when > using different force field (GROMOS UA and OPLS UA)? > > The first expression about improper didedral is a planer restriction. When > read the manual it also refers to the tetrahedral structure like this tetra > nitrogen functional group. My question is when it has > really long hydrocarbon tail, I guess it will be hard to flip over to > the mirror images. Or it is not true in the simulation?
You may take one built by other server, such as http://davapc1.bioch.dundee.ac.uk/prodrg/ as reference, and built yourself if necessary. > > Thank you very much!!! > > Best! > Xueming > > > > > > -- > 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
