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-- ============================== Department of Physical Chemistry Palacky University Olomouc tr. 17. listopadu 12, 779 00 Olomouc Czech Republic ==============================" ---------- Forwarded message ---------- From: Gustavo Seabra <gustavo.seabra.gmail.com (mailto:gustavo.seabra.gmail.com)> Date: 14 November 2012 12:40 Subject: Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d- PhoT method in AMBER12 To: AMBER Mailing List <amber.ambermd.org(mailto:amber.ambermd.org)> 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 _______________________________________________ AMBER mailing list AMBER.ambermd.org(mailto:AMBER.ambermd.org) http://lists.ambermd.org/mailman/listinfo/amber (http://lists.ambermd.org/mailman/listinfo/amber) " _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Nov 14 2012 - 09:30:03 PST