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
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