Dear Marawan,
I don't know about your specific combination of QM and MM level, but the
difference you see between pure MM, DFTB/MM and PBE/MM may originate (in
part) from the fact that different QM and MM levels/force-fields will have
different optimal Van der Waals (Lennard-Jones) parameters. This could
cause a (small) difference in density, as the water molecules may have a
different optimal difference form your nucleoside.
This paper may be relevant:
Pentikainen U, Shaw KE, Senthilkumar K, Woods CJ & Mulholland AJ (2009)
Lennard-Jones Parameters for B3LYP/CHARMM27 QM/MM Modeling of Nucleic Acid
Bases. Journal of Chemical Theory and Computation 5: 396-410
Hope this helps,
Marc
On 3 December 2012 09:02, marawan hussain <marawanhussain.yahoo.com> wrote:
> Dear AMBER users,
> I'm running an NPT QM/MM simulation using the AMBER/ORCA interface using
> PBE for the QM system. The system is composed of a nucleosde (QM) dissolved
> in a 20 A water box (MM).The system is equilibrated in the NPT ensemble
> classically and using also DFTB as implemented in AMBER. I'm using spcfw
> water model and 0.5 fs time step and no shake..I'm noticing that the dipole
> moment of the QM region is lowered by time and also the system density. At
> the first period the dipole moment is more than (10 D) which as i
> understand a result for the presence of the water molecules which increases
> the dipole moment. Afterthat, after around 2000 timesteps (almost 1 ps) the
> dipole moment is decreased and also the density. Density drops from (1.0097
> to 0.9929 ), also the volume increase a little bit (104011.5218 to
> ====> 105806.9653). i visualized the trajectory and i didn't find anything
> problematic. Could you please comment.
> I'm using periodic boundary conditions. I'm allowing the water molecules
> flexibility..Below is the input.
> Regards
> Marawan
>
> system equilibration qm-mm
> &cntrl
> imin = 0,
> ntpr = 1,ntwx = 1, ntwr = 1000,
> nstlim = 6000,dt = 0.0005,
> tempi = 300.0, temp0 = 300.0,
> ntb=2, ntp=1, taup=1,
> ntr = 0,
> cut = 15.0, ig=-1,jfastw=4,
> ntt = 3, gamma_ln = 10.0, ifqnt=1
> &end
> &qmmm
> qmmask=':1'
> qmcharge=0,
> qm_theory='EXTERN',
> qmcut=15.0,
> qm_ewald=0
> &end
> &orc
> use_template=1,
> ntpr=1,
> num_threads=8,
> dipole=1
> &end
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Received on Mon Dec 03 2012 - 01:30:03 PST
