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

[Justin A. Lemkul]

Vitaly V. Chaban 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
> "
> 

This section exists in a .tdb file, and analogous entries are in the .rtp for 
use by pdb2gmx.  Recognizing an [impropers] directive simply leads to an 
additional, separate, [dihedrals] directive written to the topology.

> 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?

The parameters you quote come from ffencadvbon.itp, which also contains this 
helpful tidbit:

; Encad out-of-plane potentials are the same functional form as
; Gromacs proper dihedrals (i.e. cosine, but with shifted sign).
; Note that the atom order is different too; In Gromacs, the first atom
; of an improper is the center one, while it is the 3rd in Encad.

Each ff*bon.itp file tends to have some information about the implementation of 
impropers in each force field, this is just one example.

> 
> I would also be very grateful if somebody could share some topology
> with improper angles to understand how it works.

You could try a couple of model structures (simple peptides/proteins) under the 
force field you want to use and get some examples by mapping the atom numbers 
back to the structure.

-Justin

> 
> Vitaly
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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