Thank you for your reply, Lina. I did try the prodrg server before. For A molecule, there is no improper dihedral. A just has one dihedral for the head group. For B molecule, it gives improper dihedral of the tetra nitrogen. I am wondering what is the criteria or at least a guidance of what could be the best choice for the topology file. Or any choices could be right and I have to try which one provide consistent results with experiment by trial?
Best! Xueming On Sun, Nov 13, 2011 at 9:57 AM, lina <lina.lastn...@gmail.com> wrote: > 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 >
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