[gmx-users] Topology dihedral or improper dihedral

[XUEMING TANG]

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.lastname at gmail.com> wrote:

> On Sun, Nov 13, 2011 at 10:26 AM, XUEMING TANG <yujan2007 at 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
> >
> >
> >
> >
> >
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