Hi Vojtech,
Just to eliminate possibilities: Have you tried a different QM hamiltonian? Does the same thing happen?
Anyways, how did you parametrize the QM region?
What I usually do when running QM/MM calculations is to first energy-minimise the system, then slowly heat it to the desired temperature, all with full-MM. Only after the system is reasonably thermalised at the final temperature I turn on the QM region.
Cheers,
Gustavo Seabra
On Wed Nov 14 2012 08:05:29 Vojtech said:
> Dear all,
>
> I would like to mention here one strange issue that I have recently
> encountered in AMBER12.
>
>
>
> I try to run QM/MM MD simulation using recently implemented SE - AM1/d-PhoT
> method (abbreviation AM1/d) as the qm_theory for the QM part of molecule.
> The system is RNA-enzym (Ribozyme) and contains just NA-nucleobases, Na+
> counter-ions and rectangular box of TIP3P molecules (around 30.000 atoms in
> total). The QM region contains just one phosphate with the ribose-ring at
> one site, methoxy group on the other and 2 nucleobases within H-bond
> distance from both non-bridging oxygens of that phosphate (typically 49
> atoms). The link atoms are thereby placed instead of C-C bonds (or C-N bonds
> in case of nucleobases).
>
> Problem is that my QM region suddenly 'explodes' during initial (typically
> 50 ps-long) heating phase (constant volume, example of script at the end) as
> soon as the temperature of the system reaches ~250 K. Firstly hydrogen atoms
> and them the other QM atoms just fly apart. I have also tried different
> modifications of my input script, charmm parameters and charges (converting
> starting pdb to charmm psf file, then backwards using chamber module), more
> sequentional pre-heating with some equilibration steps and even larger QM
> regions. All modifications resulted in same error during pre-heating or just
> at the beginning of subsequent equilibration. Notably, initial QM
> minimalization fails (SCF convergency) for the system with largest QM region
> (100 atoms). I have also tried to heat the system up to 200 K only and
> thereby it 'survises' the pre-heating phase. But during the equilibration
> phase (constant pressure) same issue occurs (also suddenly, there is no hint
> of something going wrong / any possible trend in both QM/Total Energies ..
>
>
>
>
> I am very confused and will much appreciate any reply or suggestion.
>
> Thanks in advance,
> Vojtech
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Received on Wed Nov 14 2012 - 05:00:05 PST
