[gmx-users] gromacs impropers
Feenstra at chem.vu.nl
Mon Jul 22 08:50:44 CEST 2002
alexander yakovenko wrote:
> Dear all,
> Does anybody know about improper torsions in gromacs?
> I have the system:
> | ||
> 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.
> 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.
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