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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