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
--
==============================
Department of Physical Chemistry
Palacky University Olomouc
tr. 17. listopadu 12, 779 00 Olomouc
Czech Republic
==============================
Script for heating of the system:
QM/MM MD (quick) heating of system
&cntrl
imin=0, irest=0, ntx=1, ig=-1,
nstlim=50000, dt=0.001,
ntpr=200, ntwx=200,
ntb=1, cut=10.0,
ntc=2, ntf=2,
ntt=3, gamma_ln=5.0, tempi=50.0, temp0=300.0,
ifqnt=1,
/
&qmmm
qmmask=':5.129-133 | :5.148-154 | :6.155-161 | :20.617-631 | :50.1598-
1612',
qmcharge=0,
qm_theory='AM1/d'
qmshake=0,
qm_ewald=1, qm_pme=1
/
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Received on Wed Nov 14 2012 - 03:30:03 PST
