On Fri, 9 May 2014 15:49:27 -0400
David A Case <case.biomaps.rutgers.edu> wrote:
> On Thu, May 08, 2014, hannes.loeffler.stfc.ac.uk wrote:
>
> >
> > So, the following name list does converge the structure.
> >
> > &qmmm
> > qm_theory='AM1',grms_tol=0.0002,tight_p_conv=0,
> > scfconv=1.0d-9,itrmax=500,pseudo_diag=1,vshift=0.1,
> > ndiis_attempts=200,ndiis_matrices=6,maxcyc=2000,
> > qmcharge=-1,verbosity=1
> > /
>
> Thanks for the info: we should probably be suggesting use of vshift
> more prominently in the case of convergence problems.
>
> >
> > Except that the structure gets "folded" (see attachment) with the
> > carboxy groups contacting the amino groups.
>
> I suspect that these odd geometries are related to convergence
> problems. Your initial geometry converged fine, but after some steps
> of minimization, which probably involved some "folding", you ran into
> problems.
I have attached a NetCDF trajectory which shows what is going on during
geometry optimisation. The practical problem is that there is no way to
control this.
I have also attached the trajectories for two very similar structures,
ZINC03814826 and ZINC03814838. In ZINC03814826 one carboxylate group
abstracts a proton from an amino group at the far-end of the
molecule (the same happens in ZINC03814828 at HF/6-31G* with g09). The
molecule adopts an extended structure at the end of 2000 steps (not
converged to grms). In ZINC03814838 the two carboxylate groups appear
to get "decarboxylated".
Cheers,
Hannes.
--
Scanned by iCritical.
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Received on Mon May 12 2014 - 03:00:03 PDT
