PS Sorry, that should be: "water molecules may have a different optimal
*distance from* your nucleoside"
--Marc
On 3 December 2012 09:10, Marc van der Kamp <marcvanderkamp.gmail.com>wrote:
> 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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>>
>
>
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Received on Mon Dec 03 2012 - 01:30:03 PST
