[gmx-users] Improper dihedrals, which way is correct?
Justin A. Lemkul
jalemkul at vt.edu
Wed Sep 23 14:03:25 CEST 2009
Vitaly V. Chaban wrote:
> 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
; 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.
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users