[gmx-users] Re: Improper dihedrals, which way is correct?

[Vitaly V. Chaban]

Justin,

Thanks. These tidbits are too difficult for my brain to understand.
Let's make the things easier. One has the below compound.

7 -  1 - 2
     /      \
    6        3
      \       /
       5  - 4

I want the atom 7 to be located in the same plane with atoms 1 2 and
6. Then in topol.top:
[ dihedrals ]
atoms   func angle   constant
1 2 6 7   2    180      4.602


Will this line do what I want here?

Vitaly

On Wed, Sep 23, 2009 at 1:53 PM, Vitaly V. Chaban <vvchaban at gmail.com> wrote:
> Hi,
>
> I have got confused with setting up improper dihedrals in the gromacs
> topologies. In the manual (ver. 4.0) I see the section named [
> impropers ] (page 104)
> "
> [ impropers ]
> C O1 O2 CA
> "
>
> but in the example system of the peptide
> (share/gromacs/tutor/speptide) one finds defining impropers using the
> second (in the same file) [ dihedrals ] section.
> [ dihedrals ]
> ;  ai    aj    ak    al funct            c0            c1
> c2            c3
>    1    23     5     6     1    improper_X_X_C_X
>    1    23     5     7     1    improper_N_A_C1_C
>    2     5     1     3     1    improper_X_X_M3_X
>    2     5     1     4     1    improper_X_X_M3_X
>
> What is the correct way to work with improper dihedrals? I have four
> sites, then angle value and then one force constant. What should my
> topology line look like to accomplish that?
>
> I would also be very grateful if somebody could share some topology
> with improper angles to understand how it works.
>
> Vitaly
>