[gmx-users] Topology dihedral or improper dihedral

[XUEMING TANG]

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?

Thank you very much!!!

Best!
Xueming
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