[gmx-users] R-B dihedrals
nedomacho at gmail.com
Tue Apr 14 23:12:48 CEST 2015
Tried both, the (now enormous) parameters are read in correctly, nothing in
output mdp that catches my eye. No constraints used in the system,
explicitly set in mdp. Plotted the potential at 45/315 deg minimum --
definitely nonzero at 90 degrees (starting config). This has got to be the
strangest GMX issue i've ever had.
On Tue, Apr 14, 2015 at 2:38 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 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.
> 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
> > 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.
> > minimization shows no difference -- still 90 deg. I turned off vdw for
> > 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
> > The dihedral type (3) is listed correctly in the topology. A David Lynch
> > mystery.
> > Any ideas?
> > Thanks,
> > Alex
> > --
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