[gmx-users] Incorrect dihedral restraints

[David Mobley]

What version of GROMACS are you using? Also, your force constants seem
sort of small. Have you tried larger values?

David


On 3/20/07, Jonathan Khao <jkhao at ibsm.cnrs-mrs.fr> wrote:
> Hello
>
>         My goal is to make dihedral restraints on the backbone of a bent
>         alpha
>         helix to obtain its original structure. I've looked through the
>         mailing
>         list, followed the instructions, applyed some dihedrals around
>         57° but
>         the obtained dihedrals are all close to 180°.
>
>         in my Top file, i have included the following lines
>         [ dihedral_restraints ]
>         ; A  B  C   D    type   label   angle  delta   kfac    pow
>          56 58  60  73     1      6     -63.5   0       1       2
>          73 75  77  78     1      7     -57.6   0       1       2
>
>         and in the mdp file :
>         dihre                    = Simple
>         dihre-fc                 = 100
>         dihre-tau                = 0
>         nstdihreout              = 100
>
>         What am i doing wrong ?
>
>         Thanks !
>
>         Jonathan Khao
>
>
>
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