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 <[email protected]> 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
>
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