[gmx-users] Topology dihedral or improper dihedral
lina.lastname at gmail.com
Sun Nov 13 15:57:38 CET 2011
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
> B. C-C-C-C-C-C-C-N-C-C-C-C-COOH
> 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
as reference, and built yourself if necessary.
> Thank you very much!!!
> gmx-users mailing list gmx-users at gromacs.org
> 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users