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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