[gmx-users] gromacs impropers

[K.A. Feenstra]

alexander yakovenko wrote:
> 
> Dear all,
> Does anybody know about improper torsions in gromacs?
> I have the system:
>     CH3(C0)
>      |
>      CH2(C1)
>      |
>     CB(C2)=CH(C7)-CH(C6)
>      |                        ||
>     CH(C3)=CH(C4)-CH(C5)
> 
> Its work well, while I don t add C4-C3-C2-C1  improper angle.
> From  semiempirical AM1 dynamic I know, that this angle is 0,
> but adding this information to gromacs topology reduce to wrong
> simulation (the correct simulation is AM1 dynamic). After 
> energy minimization the angle C4-C3-C2-C1 is more than 30 degrees.
> Why?
> 
> The impropers topology of this molecule is:
> [ impropers ]
>  C4  C3  C2  C1  0.00   500.00

I think you have the improper definition the wrong way around,
0 degrees corresponds to a 'trans' orientation, but you will
want a 'cis' orientation which is 180 degrees.

--
Groetjes,

Anton.