[gmx-users] R-B dihedrals

[Tsjerk Wassenaar]

Hi Alex,

Maybe writing out the preprocessed topology (grompp -pp) or checking the
.tpr with gmxdump can show whether the dihedral parameters are really what
you think they are.

Cheers,

Tsjerk
On Apr 14, 2015 10:32 PM, "Alex" <nedomacho at gmail.com> wrote:

> I have a set of dihedrals described by the R-B potential, with a minimum at
> 90 degrees, and minimization indeed yielded angles very close to that.
>
> At some point, I decided to check if I can rotate the groups to another
> angle, say, 45 degrees. Simple enough, so I changed the expression. Energy
> minimization shows no difference -- still 90 deg. I turned off vdw for all
> atoms in the vicinity, set all charges to zero -- no difference. Hiked up
> the dihedral constant by three(!) orders of magnitude -- nothing.
> Commenting out these dihedrals immediately causes grompp errors, so they
> are definitely seen by the system (I tracked the errors to the atomtypes).
> The dihedral type (3) is listed correctly in the topology. A David Lynch
> mystery.
>
> Any ideas?
>
> Thanks,
>
> Alex
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